HOMER

Software for motif discovery and ChIP-Seq analysis



Old News:


(1-13-2016) Unfortunately we had some hardware problems with the server at Salk. Some of the packages, extra data files and older versions may not be available right away, but working on it.

(1-13-2016) Check out Metascape for GO/Functional enrichment analysis (http://metascape.org/).  Great replacement for DAVID for online gene list analysis!


(1-13-2016) New version v4.8.  Some of the website has been updated, but still working on that.  Will post new documentation soon.
(8-25-2014) Many upgrades and bug-fixes.  Fixed issues with strand specific read counting and sizing issues with annotatePeaks.pl.  Updates to accession numbers and GTF parsing too.

(3-29-2014) New version v4.6. Better super enhancer code, plus lots of other minor upgrades.

(1-27-2014) New version v4.5 with updated genome packages too - Last version did not correctly assign priority assignments in annotations (i.e. TSS > exons > introns > intergenic was not honored in last version - fixed now).  Problems with some of the update scripts too.  Website updates are ongoing.


(1-23-2014) Updated All Organism Packages to v1.1 - latest packages lacked the org2gene.tsv file (i.e. human2gene.tsv).  Users that updated from the older version of HOMER probably didn't notice since the old files would have still been there - new users probably got an error.


(1-15-2014) Welcome to homer.salk.edu - new host for HOMER!

(1-15-2014) Lots of new documentation.  More new documentation will probably be added to the site over the next week or so, and new PDF's will be created once that gets in good shape.

(1-14-2014) New version v4.4. New version with changes to configuration to help separate the code and data, update scripts to keep annotation/accessions up-to-date and incorporate custom genomes/organisms.  As always, lots of new features and bug fixes.  It's very likely a new version will be posted soon to smooth out any details.  Major changes to note:
  1. Major Updates to annotations and custom configuration - easier to add your own genome or annotation
  2. bedGraphs and coverage histrograms are now normalized for fragment length (this is a GOOD upgrade, be careful comparing to old results)
(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...

(11-2-2012)
New version v4.1, lots of bug fixes

(10-15-2012)
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.







Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu