Alternatives and similar repositories for rock

Users that are interested in rock are comparing it to the libraries listed below

• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆41Updated last year
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 3 months ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated 2 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆61Updated 4 years ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆20Updated 2 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• markowetzlab / CINSignatureQuantification
  Quantifying copy number signatures from absolute copy number profiles
  ☆24Updated 2 months ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• mskcc / facets-suite
  Utility functions for FACETS
  ☆35Updated last year
• PhanstielLab / bedtoolsr
  R package wrapping bedtools
  ☆41Updated 2 months ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆55Updated 4 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 5 years ago
• jxzb1988 / MMQTL
  MMQTL is a statistical package applying meta-analysis to detect multiple QTL signals integrating signals among conditions, with control f…
  ☆11Updated 2 months ago
• AlexandrovLab / SigProfilerSingleSample
  SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity…
  ☆23Updated 4 months ago
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆33Updated 6 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• Danko-Lab / tutorials
  Tutorials covering various topics in genomic data analysis.
  ☆17Updated 6 years ago
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆33Updated 3 years ago
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆27Updated 3 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated 10 months ago
• stjude / ChIPseqSpikeInFree
  A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
  ☆32Updated 3 years ago
• thelovelab / rnaseqDTU
  RNA-seq workflow: differential transcript usage
  ☆21Updated last year
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆43Updated 7 years ago
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆42Updated last year
• ait5 / CNApp
  CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…
  ☆20Updated 5 years ago
• nuno-agostinho / psichomics
  Interactive R package to quantify, analyse and visualise alternative splicing
  ☆37Updated 2 weeks ago