Alternatives and similar repositories for PureCN

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

• VanLoo-lab / ascat
  ASCAT R package
  ☆181Updated 3 months ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆132Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆115Updated 11 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆106Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 7 months ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆87Updated 9 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆108Updated 5 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆161Updated 10 months ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• sztup / scarHRD
  ☆116Updated last year
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆148Updated 10 months ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆149Updated 2 years ago
• raerose01 / deconstructSigs
  deconstructSigs
  ☆141Updated 2 years ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆171Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆219Updated last year
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆113Updated 2 years ago
• guigolab / ggsashimi
  Command-line tool for the visualization of splicing events across multiple samples
  ☆130Updated 11 months ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 4 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆110Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 7 months ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆114Updated 4 months ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆124Updated 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…
  ☆77Updated 5 years ago