Software for motif discovery and ChIP-Seq analysis

Old News:

(8-26-2013) New version v4.3.  Lots of new features including scripts for processing files in batch.  Bug fixes too!

(4-11-2013) New version v4.2, lots of updates and bug fixes.  Many of the genome versions and annotations etc. have been updated (or are currently being loaded on the website). Pombe & rice genomes have been added.  Arabidopsis has been reconfigured to use Ensembl-style chromosome names (i.e. "1" not "Chr1" as the last homer version used.  Sorry in advance!).  Additional documentation will be added soon...

New version v4.1, lots of bug fixes

New version v4.0!  Full integration of Hi-C analysis routines, updated annotation files, plus minor bug fixes and updates.  Lots of updated documentation too.(10-2-2012) New version v3.18 Several small bug fixes. Little behind on documentation updates, coming soon...

(8-2-2012) New version v3.15 Added analyzeRepeats.pl for better repeat quantification, added options to configureHomer.pl script and config.txt file to store web server information for bigWigs and hubs, minor bug fixes.

(7-20-2012) New version v3.14 Added species specific motif libraries (tries to auto detect, -mset option in findMotifs.pl/findMotifsGenome.pl), modernized the analyzeChIP-Seq.pl script, added suppport for input-normalized bedGraph files

(7-18-2012) New version v3.13.1 Added some mC/C support, updated motif library, bug fixes

(6-22-2012) New version v3.13 - Lots of updates, including better/updated annotation, including use of single annotation for each genome verion [removal of 'separate' masked genomes] (can use hg18r for hg18 or add "-mask" to most commands and it sill still figure it out). ALL promoters/genomes must be updated to work with the new version. Also added support for mm10, rn5, ce10, sacCer3, and xenTro3 Change Log

(6-8-2012) New version v3.12 - Fixed bug in mergePeaks, other small bugs

(5-21-2012) New version v3.11 - mostly small fixes and bugs.

(3-22-2012) New version v3.10 - mostly small fixes.

(2-1-2012) New version fixes issue with HOMER-created bigWig files.  UCSC Genome Browser updated their bigWig file processing on Feb 1st, which caused errors with bigWig files created previously with HOMER.  The problem has been fixed, but you may need to remake your bigWig files with the new version for them to work.

(11-30-2011) Minor update (v3.8.1) for motif finding (parsing of small sequences) and support for variable region histograms (i.e. gene body)

(11-29-2011) New version v3.8 with bug fixes, added UCSC multi-wig hub support (makeMultiWigHub.pl), added support for Arabidopsis (tair10) and X. tropicalis (xenTro2), and added general support for genomes composed of scaffolds. 

(10-12-2011) The new version (v3.5/v3.6) fixes errors in the mergePeaks program that arise when merging peaks over large distances, also added "-nfr" option to findPeaks to identify nucleosome free regions more effectively.  Cleaned up peak overlap significance calculations, and added Benjamini multiple-hypothesis testing corrections to various programs such as known motif enrichment.

(09-30-2011) The new version (v3.4) - fixes error in motif percentages reported after de novo motif finding.  Previous version calculated motif percentages using sequence with more significant motifs masked, causing some instances to be missed.  HOMER now reports the % of sequences containing the sequence using the original sequences.  The motifs found by the algorithm themselves are unaffected, just the reported statistics have changed.

(05-25-2011) The new version (v3.1) is much more "custom" genome friendly - allows you to directly specify genome sequence files instead of "configuring" genomes.

(05-20-2011) Added Yeast (sacCer2) and zebrafish (danRer7).  Also restructured accession number/gene annotation information such that it is tied to the "promoters" of a given organism.  This way you don't have to download all of it with the main program.

(05-09-2011) First major update of HOMER in a while (v3.0).  Most importantly, the motif finding has been rewritten to improve accuracy and performance, with multiprocessor support.  Pretty much everything else has also been worked on and improved.  GC-normalization, GRO-Seq (nascent RNA) analysis, RNA motif analysis, and a number of other routines have been added.

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