Alternatives and similar repositories for deconstructSigs

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

• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• chrisamiller / fishplot
  Create timecourse "fish plots" that show changes in the clonal architecture of tumors
  ☆171Updated last week
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆98Updated last year
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆158Updated last week
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆121Updated 2 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆89Updated 8 years ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆149Updated 5 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆105Updated 4 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆94Updated 8 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆62Updated 5 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆73Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆124Updated 5 years ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆88Updated 5 years ago
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆113Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 5 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆142Updated 5 months ago
• parklab / ShatterSeek
  ☆75Updated 2 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆78Updated 5 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆110Updated 5 years ago
• guigolab / ggsashimi
  Command-line tool for the visualization of splicing events across multiple samples
  ☆136Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆124Updated this week
• sztup / scarHRD
  ☆119Updated 2 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆120Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 5 months ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆231Updated 8 months ago