GersteinInfo - User contributions [en]

NCVAR

2011-06-01T15:26:26Z

Xm24:

'''ncVAR'''

Mu, X.J., Lu, Z.J., Kong, Y., Lam, H.Y. and Gerstein, M.B. (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. ''Nucleic Acids Res.'', doi: 10.1093/nar/gkr342. [http://nar.oxfordjournals.org/content/early/2011/05/19/nar.gkr342.full Full text]

Specifications for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

NCVAR

2011-06-01T15:25:14Z

Xm24:

'''ncVAR'''

Mu, X.J., Lu, Z.J., Kong, Y., Lam, H.Y. and Gerstein, M.B. (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. ''Nucleic Acids Res.'', doi: 10.1093/nar/gkr342.

Specifications for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

NCVAR

2011-06-01T15:17:58Z

Xm24:

'''ncVAR'''

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Xinmeng Jasmine Mu; Zhi John Lu; Yong Kong; Hugo Y. K. Lam; Mark B. Gerstein
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr342

Specifications for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

NCVAR

2011-04-19T15:33:02Z

Xm24:

'''ncVAR'''

Mu et al, ''in preparation''

Specifications for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

Public wiki pages linked from elsewhere

2011-04-19T15:32:37Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[NCVAR]] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

Public wiki pages linked from elsewhere

2011-04-19T15:32:20Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[NCVAR]] page
* [['''ncVAR''']] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

Public wiki pages linked from elsewhere

2011-04-19T15:31:54Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[NCVAR]] page
* [['''ncVAR'''test]] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

NCVAR

2011-04-19T15:31:09Z

Xm24:

NCVAR

2011-04-19T15:30:51Z

Xm24:

'''ncVAR'''

Mu et al, ''in preparation''

Specificity for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

NCVAR

2011-04-19T15:30:19Z

Xm24:

'''ncVAR'''
Mu et al, ''in preparation''

Specificity for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

NCVAR

2011-04-19T15:28:29Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]

NCVAR

2011-04-19T15:27:02Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]
DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]

NCVAR

2011-04-19T15:23:17Z

Xm24:

NCVAR

2011-04-19T15:20:16Z

Xm24:

NCVAR

2011-04-19T15:16:39Z

Xm24:

NCVAR

2011-04-19T15:16:04Z

Xm24:

NCVAR

2011-04-19T15:13:33Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz download]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz download]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz download]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz download]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz download]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz download]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz download]
PolII
DNase

NCVAR

2011-04-19T15:11:56Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz download]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz download]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz download]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz download]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz download]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz download]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz download]
PolII
DNase

Gene 874 0.87 6.96E-09
CDS 4 0.04 3.47E-24
5'UTR Only 92 0.95 3.11E-01
3'UTR Only 10 0.46 6.16E-03
Intron Only 653 0.99 3.57E-01
Whole CDS(s) 0 0.00 1.24E-14
Partial CDS(s) 4 0.09 1.17E-10
Whole Gene(s) 0 0.00 2.34E-01
Partial Gene(s) 874 0.87 7.75E-09
Single whole gene 0 0.00 2.37E-01
Multiple whole genes 0 0.00 4.56E-01
2 whole genes 0 0.00 4.58E-01
3 whole genes 0 0.00 4.89E-01

NCVAR

2011-04-19T15:11:30Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz download]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz download]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz download]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz download]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz download]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz download]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz download]
PolII
DNase

Gene 874 0.87 6.96E-09 0.89
CDS 4 0.04 3.47E-24 0.04
5'UTR Only 92 0.95 3.11E-01 0.95
3'UTR Only 10 0.46 6.16E-03 0.50
Intron Only 653 0.99 3.57E-01 1.02
Whole CDS(s) 0 0.00 1.24E-14 0.00
Partial CDS(s) 4 0.09 1.17E-10 0.09
Whole Gene(s) 0 0.00 2.34E-01 0.00
Partial Gene(s) 874 0.87 7.75E-09 0.89
Single whole gene 0 0.00 2.37E-01 0.00
Multiple whole genes 0 0.00 4.56E-01 0.00
2 whole genes 0 0.00 4.58E-01 0.00
3 whole genes 0 0.00 4.89E-01 0.00

NCVAR

2011-04-19T14:58:57Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz download]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz download]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz download]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz download]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz download]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz download]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz download]
PolII
DNase

NCVAR

2011-04-19T14:58:26Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz download]
STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz download]
NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz download]
c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz download]
c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz download]
c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz download]
JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz download]
PolII
DNase

NCVAR

2011-04-19T14:37:43Z

Xm24:

NCVAR

2011-04-19T14:34:07Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

''TF motif'' ''Track'' ''jkfjd''
CTCF test
STAT1 test

NCVAR

2011-04-19T14:24:50Z

Xm24:

Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser

CTCF test
STAT1 test

NCVAR

2011-04-19T14:22:29Z

Xm24:

test main

CTCF test
STAT1 test

NCVAR

2011-04-19T14:21:18Z

Xm24:

The Mapped Read Format (MRF) flat file consists of '''three''' components and this format is closely associated with the software components of [http://rseqtools.gersteinlab.org RSEQtools]

CTCF test
STAT1 test

Public wiki pages linked from elsewhere

2011-04-16T05:37:09Z

Xm24:

Public wiki pages linked from elsewhere

2011-04-16T05:36:47Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[_ncVAR]] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

Public wiki pages linked from elsewhere

2011-04-16T05:33:06Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[ ncVAR]] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

--ncVAR--

2011-04-16T05:31:40Z

Xm24: Created page with 'hello'

hello

Public wiki pages linked from elsewhere

2011-04-16T05:31:32Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[--ncVAR--]] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

NCVAR

2011-04-16T05:30:59Z

Xm24: Created page with 'Hello'

Hello

Public wiki pages linked from elsewhere

2011-04-16T05:30:40Z

Xm24:

Public wiki pages linked from elsewhere

2011-04-16T05:25:21Z

Xm24:

These pages have been first established on the wiki are best accessed first from outside the wiki.
These link collection is fairly random.

*[[cs545-07]] : Course page for CS545
*[http://wiki.gersteinlab.org/pubinfo/Human_TF_List Human Transcription Factors] page
*[[Motions Supplement]]
*[[Other Papers]] than those shown on [http://papers.gersteinlab.org "papers page"]
*[[Calendar]]
*[[AlleleSeq]] documentation
* Additional Info for Mark
** [[contact information]] beyond that in http://contact.gerstein.info
** [[outbox information]] beyond that in http://outbox.gerstein.info
** Description of Mark Gerstein's Research ([http://gersteinlab.org/about main]) ([[MBG-Profile|extra stuff]])

* [[Lab Address]] + [[Some Useful Email Addresses]]
* Random other links
**[http://bioinfo.mbb.yale.edu/stats Web Page Access Statistics]
* [[Old lectures and courses]]
* [[Null Page]]

*[[RSEQtools]]: a computational suite for the analysis of RNA-Seq data including a compact and "privacy-aware" data format.
*[[FusionSeq]]: a computational framework to identify fusion transcripts from paired-end RNA-Seq data.
*[[ACT Tool]]: for aggregation and correlation analyses of genomic signal tracks
*[[PeakSeq]]: a computational tool for analyzing ChIP-Seq data
* [[Papers Page Code]]
* [[ncVAR]] page

===Software and tools===
*[[Cbb752b11]]: CBB 752b in 2011
----

Tool ncVAR

2011-04-14T14:11:43Z

Xm24:

hi there
haha