The Good Doctor - Season 4 | ...

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

The Good Doctor - Season 4 | ...

: A significant portion of the season is dedicated to Shaun and Lea’s evolving relationship, including a major pregnancy arc. This shift divided fans; some enjoyed the emotional intimacy, while others felt the "Lea drama" overshadowed the medical cases.

: Shaun transitions from being a student to a supervisor, overseeing a new group of first-year residents. Critics noted that while this provided character growth, it sometimes felt repetitive or detracted from Shaun's personal medical genius moments. The Good Doctor - Season 4 ...

: The season begins with a two-part premiere addressing the COVID-19 pandemic. While some praised its realism, others found it difficult to watch or preferred to use TV as an "escapism" from real-world events. : A significant portion of the season is

: Many audience reviews on platforms like Rotten Tomatoes and Reddit criticized the season for feeling "overly political," tackling issues such as systemic racism, gender identity, and medical ethics in a way that some felt was "heavy-handed". Performance and Ratings Critics noted that while this provided character growth,

Program Components and Older Versions

homer2 program - key executable for HOMER motif discovery (homerCppOnly.*.zip). (This archive actually contains all of the c++ executable, not just homer2). Unzip in the desired directory and simply type "make" to compile the program.

The configuration script really doesn't deal with older versions, but you can download older versions yourself should you really feel like using inferior data or software!

Old Versions of HOMER Software
Old Versions of Organism Packages
Old Versions of Promoter Packages
Old Versions of Genome Packages

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)

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