Elementolab/ChIPseeqer versions

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Elementolab/

ChIPseeqer versions

Work-in-progress (next release) - AVAILABLE IN THE SVN

1. (to-do) Fix conservation for mm9. Change the naming format of the conservation files.

   (to-do) Allow vertebrates conservation scores.

   (to-do) If there is wrong path in CSReadCountMatrix, don't output the label column

   (to-do) Fix error caused by missing --desc in CSReadCountMatrix

   (to-do) Make CSCompareIntervals faster (mainly the making of the random regions - how? not use CSAnnotate any more?)

   (to-do) Update GUI for find_peaks_and_genes_in_pathway after running PAGE (very useful now that it can export genes for all pathways - updated script)

Released

1. ChIPseeqer-2.1 Download

   Support for hg19, mm9, mm10, zv9, rn4 (ChIPseeqer, ChIPseeqerAnnotate, ChIPseeqerFIRE, ChIPseeqeriPAGE, ChIPseeqerNongenicAnnotate)

   Fixed error with EXONS column, in ChIPseeqerAnnotate results

   Fixed compilation error caused by values.h in tools/KOHONEN/kohonen.c

   dist/SCRIPTS/find_peaks_and_genes_in_pathways works for all pathways, if pathway is not set by user.

   Fixed segmentation fault in ChIPseeqer.bin when -chrdata not used. Actually, make -chrdata used in all cases.

   ChIPseeqer.bin throws error message when cannot access memory while reading reads. Tested with wrong chrdata file. (e.g., hg19 data with hg18.chrdata).

   CSAnnotate throws error message when annotation files are missing.

   Fixed bed file import (no need for the U0 column). It works as long as 6th column is the strand (output of BamToBed from bedTools)

2. ChIPseeqer-2.0 - Download (Known issues and how to address them)

   Installation fixes

   Fixed memory leaks

   Added program FindGenomeFractions

   Added INTERGENIC category in ChIPseeqerAnnotate

   Added script ChIPseeqerCompareIntervals

   Added script ChIPseeqerCreateRandomRegions

   Statistical support for CompareIntervals

   Added "CGI" option in ChIPseeqerFIRE

   ChIPseeqerCons, support for mm9

   Statistical support for Kohonen

   Added Reactome pathways in iPAGE

3. ChIPseeqer-1.0 - Download

   Graphical user interface (GUI) for basic tools

   Supporting species: hg18, mm9, dm3, saccer

   Supporting annotations: refSeq, AceView, Ensembl, UCSCGenes