uci-cbcl / EXTREMEView external linksLinks
An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data
☆32May 22, 2018Updated 7 years ago
Alternatives and similar repositories for EXTREME
Users that are interested in EXTREME are comparing it to the libraries listed below
Sorting:
- Yet Another Motif Discovery Algorithm☆53Jan 10, 2019Updated 7 years ago
- rust external sort algorithm implementation☆20May 9, 2025Updated 9 months ago
- Nanopore desc☆18Aug 22, 2016Updated 9 years ago
- Basic, no assumptions, multi-pileup☆24Mar 26, 2014Updated 11 years ago
- Analyzes whole genome sequencing data for gene-editing verification☆10Feb 6, 2026Updated last week
- Expedite large-scale identification of CNVs within predefined genomic regions. Online app available for those with GP2 Tier 2 Access.☆12Jun 13, 2025Updated 8 months ago
- ☆10Jun 21, 2015Updated 10 years ago
- localised duplicate detection on patterned flow cells☆10Feb 27, 2019Updated 6 years ago
- A JBrowse plugin for creating sashimi or junction style plots from RNA-seq data☆14Apr 30, 2021Updated 4 years ago
- Import and run CWL workflows on DNAnexus (alpha)☆13Sep 12, 2018Updated 7 years ago
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated last month
- POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction☆11Jan 16, 2025Updated last year
- robust matching of small variant datasets using flexible scoring schemes☆11Mar 26, 2020Updated 5 years ago
- Robust individual and aggregate checksums for nucleotide sequences☆17Updated this week
- Rapid competitive read demulitplexer. Made with tries.☆23May 19, 2025Updated 8 months ago
- Fast interval intersection library☆44Aug 20, 2025Updated 5 months ago
- Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.☆52Jun 5, 2018Updated 7 years ago
- Variant call adjudication☆16Jun 13, 2024Updated last year
- KAUST Assembly Read Error Correction Tool☆15Aug 15, 2015Updated 10 years ago
- DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR☆18May 12, 2022Updated 3 years ago
- SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis☆25Apr 7, 2015Updated 10 years ago
- A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.☆18Jan 16, 2026Updated 3 weeks ago
- Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)☆18Oct 12, 2025Updated 4 months ago
- A program for summarising CpG methylation patterns☆20Sep 9, 2016Updated 9 years ago
- do multiple nucleotide sequence alignment fast and accurately☆18Dec 1, 2022Updated 3 years ago
- Visualization tool for temporal clonal evolution.☆18Mar 13, 2020Updated 5 years ago
- Tools to gather evidence for structural variation via breakpoint detection.☆19Jan 21, 2026Updated 3 weeks ago
- A sequence demultiplexer for the Illumina HiSeq technology☆21Apr 29, 2013Updated 12 years ago
- Toolkit for constructing, analyzing, and visualizing data-driven ontologies☆17Feb 10, 2023Updated 3 years ago
- Minor Variant Calling and Phasing Tools☆15Jan 13, 2022Updated 4 years ago
- Variant Caller Analysis Dashboard and Data Management System☆36Feb 8, 2016Updated 10 years ago
- Reference bias measuring toolkit☆20Apr 18, 2025Updated 9 months ago
- Hotspot is a program for identifying genomic regions of local enrichment of short-read sequence tags.☆16Apr 12, 2014Updated 11 years ago
- Human mitochondrial variants annotation using HmtVar.☆18Oct 16, 2023Updated 2 years ago
- Hera-T, a fast and accurate tool for estimating gene abundances in single cell data generated by the 10X-Chromium protocol☆18Nov 9, 2021Updated 4 years ago
- Method for identifying trait-relevant gene annotations from GWAS summary statistics.☆18Jun 29, 2022Updated 3 years ago
- A command line utilty for working with BINSEQ files☆35Jan 30, 2026Updated 2 weeks ago
- Deduplication based on custom inline DNA barcodes.☆21Aug 17, 2018Updated 7 years ago
- Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.☆20Updated this week