Desi Choot Chudai Ladki Ki Batein -

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

Desi Choot Chudai Ladki Ki Batein -

At midnight, the city does not sleep. It hums. A low, continuous thrum of life. A last chai is served. A dog barks. The koel has gone silent.

The corner shop sells SIM cards next to beedis (hand-rolled cigarettes) and packets of Maggi noodles . The sign above reads: “All Types of Repairing & Chai.” Desi choot chudai ladki ki batein

By 8:00 AM, the street is a symphony of contradictions. An auto-rickshaw painted with “Horn OK Please” and a picture of a tiger weaves past a Mercedes. A cow, serene and meditative, sits in the middle of the road while a man in a neon safety vest takes a selfie with it. A young woman in a saree (pallu flapping like a saffron flag) rides an electric scooter, one hand on the throttle, the other balancing a steel tiffin box that holds her husband’s lunch. At midnight, the city does not sleep

Inside the kitchen, a mother grinds fresh coconut on a black sil-batta (stone grinder). The sound is rhythmic—a low, guttural scratch that has been the same for 5,000 years. No blender can replace it. The air smells of simmering ghee , curry leaves popping in hot oil, and the faint, sacred smoke of sambrani (frankincense) from the tiny shrine in the corner. A last chai is served

Children fly kites from rooftops, shouting “ Bo kata! ” when they cut another’s string. A bangle-seller walks by, his wooden cart full of shimmering glass circles in every color of a wedding mandap . A group of uncles sits on plastic chairs outside a tea stall, solving the world’s problems over cutting chai (half a glass, because full is too much).

India is not a place. It is a verb. It is happening. Loudly, softly, messily, and with an unshakable faith that chaos will always make sense by dinner .

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