Elementolab/

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	* '''Resources'''		* '''Resources'''
		+	** [https://sites.google.com/site/epiworkshop2012/ Epiworkshop 2012]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/2011_CSHL Elemento lab participation in CSHL 2011 Summer School]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/2011_CSHL Elemento lab participation in CSHL 2011 Summer School]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/R_tutorial R tutorial]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/R_tutorial R tutorial]

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Revision as of 16:55, 11 February 2012

• ChIPseeqer: A comprehensive framework for the analysis of ChIP-seq data
  • Installation Instructions
  • FAQ
  • Versions
  • Graphical User Interface version
    • Tutorial
  • Command-line version
    • Tutorial
    • Supported formats
    • Supported species (and how to add new ones)
  • LATEST NEWS
    • [07/23/2011] Our recent ChIPseeqer paper in BMC Bioinformatics 2011, 12:277 has been highlighted as
    • [07/07/2011] The ChIPseeqer publication is out! An integrated ChIP-seq analysis platform with customizable workflows Eugenia G Giannopoulou and Olivier Elemento, BMC Bioinformatics 2011, 12:277.
    • [06/22/2011] ChIPseeqer v2.0 known issues and how to address them.
    • [05/23/2011] ChIPseeqer v2.0 is out! Check out the Installation Instructions.
    • [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.
    • Older news.

• 3D chromosome structure visualization
  • Project page

• Visualizing functional links among sequencing variants using VizVar
  • Project page

• SNVseeqer: Single Nucleotide Variant and mutation detection from RNA-seq and DNA-seq data
  • Installation Instructions
  • Tutorial
  • Mutation-related Resources

• FIRE: Finding Informative Regulatory Elements
  • Download at https://tavazoielab.c2b2.columbia.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 https://tavazoielab.c2b2.columbia.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.c2b2.columbia.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

• FIREpro: Ab initio discovery of protein regulatory motifs
  • FIRE-pro web site
  • FIRE-pro paper in PLoS ONE
  • Usage notes
  • Protein Motif Resources

• Resources
  • Epiworkshop 2012
  • Elemento lab participation in CSHL 2011 Summer School
  • R tutorial
  • Subversion Source Browser
  • GenRegexp
  • C/C++ Programming
  • Perl tips
  • Tutorial for various tools (clustering, etc)
  • ICB/Elementolab Subversion tutorial
  • Datasets
  • Unix/Mac tips
  • Deep Sequencing Resources
  • Gene Identifiers
  • Formats
  • Elementolab/Peak Finding with Promoter Arrays
  • Elementolab/PBM Motifs
  • Tips on using the Panda computer cluster
  • Compute genome mappability
  • Web Application Design
  • QT Tips
  • Image analysis
  • Database of Cancer Drug Resistance Mutations
  • Computing RPKM values from RNA-seq data
  • Big Data

• Funding
  • Format changes for R01s http://grants.nih.gov/grants/guide/notice-files/NOT-OD-09-149.html
  • Tips for revising an NIH grant http://scientopia.org/blogs/drugmonkey/2011/08/29/structural-aspects-of-revising-your-nih-grant/
  • 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
  • Microsoft Research Fellow http://research.microsoft.com/en-us/collaboration/awards/msrff_application.aspx
  • Google Research Awards http://research.google.com/university/relations/research_awards.html
  • Sidney Kimmel Scholar (deadline Dec 1) http://www.kimmel.org/Application_Process37.html
  • Human Frontiers (deadline ~ mid-March) http://www.hfsp.org/funding/research-grants/information-and-guidelines
  • James McDonnell Foundation (deadline: March 15): http://www.jsmf.org/apply/research/index.htm
  • Brain Tumor Foundation http://www.braintumor.org/research/funding-opportunities/

• 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