Sivr 171 Upd -

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

Sivr 171 Upd -

I’ll assume you want a feature enhancement request for SIVR 171 (update). Here’s a concise feature proposal you can use or submit. Feature Title SIVR-171: Interactive Update Workflow for Content Synchronization Summary Add an interactive update workflow that safely synchronizes content changes across environments with preview, conflict resolution, and rollback capabilities. Goals

Reduce failed updates and merge conflicts. Let users preview changes before applying. Provide easy rollback and audit trail.

User Story As a content manager, I want to preview and selectively apply updates from staging to production, resolve conflicts during synchronization, and rollback if needed so I can avoid downtime and data loss. Scope & Requirements Core

Preview: show a diff view (field-level) between source and target. Selective apply: allow per-item or per-field apply/reject. Conflict detection: detect concurrent changes and surface conflicts with side-by-side comparison. Approval flow: optional multi-step approvals before apply. Rollback: store pre-update snapshot to revert within N days. Audit log: record user, timestamp, and change summary. sivr 171 upd

Non-functional

Must complete preview within 3s for up to 10k items. Secure: respect current access controls. Incremental: support partial syncs.

UI/UX

Modal diff panel with inline edit and accept/reject toggles. Bulk actions (accept all, reject all). Visual conflict badges and suggested merges.

API

Endpoint: POST /api/sivr/171/preview (body: sourceEnv, targetEnv, itemIds[]) Endpoint: POST /api/sivr/171/apply (body: previewId, approvals[]) Endpoint: POST /api/sivr/171/rollback (body: updateId) I’ll assume you want a feature enhancement request

Data Model Changes

PreviewRecord { id, sourceEnv, targetEnv, diffs[], createdBy, createdAt } UpdateRecord { id, previewId, status, appliedBy, appliedAt, rollbackAvailableUntil }

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