Elementolab/

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Revision as of 18:00, 4 April 2011

ChIPseeqer: A comprehensive framework for the analysis of ChIP-seq data
- Installation Instructions
- Graphical User Interface version
  - Tutorial
- Command-line version
- LATEST NEWS!
  - [02/17/2011] ChIPseeqer now available as a user-friendly graphical interface! Check out the Installation Instructions and Tutorial
  - [01/29/2011] Want to overlap your peaks with other ChIP-seq datasets from Encode? Use option --type=Encode and --TFname=select_TF in ChIPseeqerNongenicAnnotate to get the peaks overlap with a specific ChIP-seq dataset from ENCODE.
  - [12/09/2010] Added the support of RNAGenes annotation. Use ChIPseeqerRNAGenes to get the peaks overlap with known RNA genes.
  - [12/08/2010] ChIPseeqer now also supports the Ensembl annotation (for hg18-human, mm9-mouse and dm3-drosophila), the AceView annotation (for mm9-mouse) and the UCSCGenes annotation (for hg18-human, mm9-mouse)
  - [10/18/2010] ChIPseeqer basic analysis (peak detection, gene annotation) is now also available for Saccharomyces cerevisiae. Use -chrdata DATA/sacser.chrdata option in ChIPseeqer and --genome=sacser option in ChIPseeqerAnnotate and ChIPseeqerSummaryPromoters
  - Older news

SNVseeqer: Single Nucleotide Variant and mutation detection from RNA-seq and DNA-seq data

FIRE: Finding Informative Regulatory Elements
- Download at http://tavazoielab.princeton.edu/FIRE or get it from our subversion repository : svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/FIRE/trunk FIRE/ (restricted to ICB)
- Tutorial at http://tavazoielab.princeton.edu/FIRE/tutorial.html
- Frequently Asked Questions about FIRE
- Fast Promoter Extraction

iPAGE: Pathway Analysis of Gene Expression
- Primary download page with GUI, etc is http://tavazoielab.princeton.edu/iPAGE
- Alternative download with ElementoLab-specific functions, databases, etc at http://physiology.med.cornell.edu/faculty/elemento/lab/files/PAGE.zip
- from our subversion repository (ICB): svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/PAGE/trunk PAGE/ (restricted to ICB)
- from our subversion repository (everybody else): svn co --username=guest --password=email@email.com https://pbtech-vc.med.cornell.edu/public/svn/elementolab/PAGE/trunk PAGE/
- PAGE Tutorial
- Howto: add new pathway database to PAGE

Funding
- Format changes for R01s http://grants.nih.gov/grants/guide/notice-files/NOT-OD-09-149.html
- Documents http://grants.nih.gov/grants/funding/phs398/phs398.html
- Damon Runyon-Rachleff Innovation Award http://www.damonrunyon.org/for_scientists/more/innovation_award_overview
- Stand Up to Cancer http://www.aacr.org/home/public--media/stand-up-to-cancer/grant-giving-model-and-expert-review-process/su2c-innovative-research-grants.aspx
- Illumina IDEA challenge http://www.illumina.com/landing/idea/
- LLS TRP http://www.leukemia-lymphoma.org/all_page.adp?item_id=11620

Working at Cornell
- J-1 Waiver rules http://www.isso.cornell.edu/academicstaff/jwaiver.php

Events
- The Rockefeller Calendar of Events is the most comprehensive list of seminars in the tri-Inst area
- NextGen JC organized by Fabien
- Epigenomics meetings organized by Olivier

 ** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/QT_Tips QT Tips]
 ** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Image_Analysis Image analysis]
+** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/RNA-seq_RPKMs Computing RPKM values from RNA-seq data]