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[s1e3] Smile, Or Go To Jail -

Software for motif discovery and next generation sequencing analysis

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Hardware Requirements (recommended): 2+ Gb memory (4-8+ Gb), 10+ Gb Hard Drive space (50+ Gb)
Software Requirements: Unix compatible OS (or cygwin), perl, gcc, make, wget (optional for full functionality: R, DESeq2, blat, bedGraphToBigWig, liftOver)
License: GPLv3

HOMER works on pretty much any Linux/UNIX systems, including MacOS (if Xcode compilers are installed) and on Windows using either cygwin or a Linux subsystem.

If you are looking specifically for HOMER2, you are in the right place! HOMER2 is integrated into HOMER.

Full Program Download

: Detective Nate Lahey investigates Sam Keating’s alibi for the night of Lila Stangard's murder. He discovers the alibi does not check out but lies to Annalise , telling her Sam was where he claimed to be.

The "case of the week" follows Paula Murphy (guest star Ana Ortiz ), a suburban "soccer mom" arrested for a minor misdemeanor. However, as she is about to be released, she is rearrested by the FBI under an alias for a 1994 felony murder involving a bombing. Annalise Keating and her students must prove her innocence, which hinges on the testimony of another suspect in that decades-old case.

: Wes Gibbins’ determination leads Annalise to officially take on Rebecca Sutter as a client.

Program Components and Older Versions

[s1e3] Smile, Or Go To Jail -

: Detective Nate Lahey investigates Sam Keating’s alibi for the night of Lila Stangard's murder. He discovers the alibi does not check out but lies to Annalise , telling her Sam was where he claimed to be.

The "case of the week" follows Paula Murphy (guest star Ana Ortiz ), a suburban "soccer mom" arrested for a minor misdemeanor. However, as she is about to be released, she is rearrested by the FBI under an alias for a 1994 felony murder involving a bombing. Annalise Keating and her students must prove her innocence, which hinges on the testimony of another suspect in that decades-old case. [S1E3] Smile, or Go to Jail

: Wes Gibbins’ determination leads Annalise to officially take on Rebecca Sutter as a client. : Detective Nate Lahey investigates Sam Keating’s alibi


Update Information

Change Log - Short description of recent changes

update.txt - Current HOMER configuration list (Currently support human hg17/hg18/hg19, mouse mm8/mm9, rat rn4, X. tropicalis xenTro2, drosophila dm3, and C. elegans ce6, Zebrafish danRer7, yeast sacCer2, Arabidopsis tair10, Rice msu6, Pombe ASM294v1)
[S1E3] Smile, or Go to Jail
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu