Alternatives and similar repositories for Manuscripts:

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

• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated 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…
  ☆19Updated 5 years ago
• McGranahanLab / TcellExTRECT
  ☆47Updated last month
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• UMCUGenetics / primary-met-wgs-comparison
  Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.
  ☆15Updated last year
• markowetzlab / CINSignatureQuantification
  Quantifying copy number signatures from absolute copy number profiles
  ☆23Updated this week
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 3 years ago
• ChongJenniferZhang / CLCA_WGS
  ☆24Updated last year
• getzlab / MutSig2CV
  MutSig2CV from Lawrence et al. 2014
  ☆31Updated 4 years ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆29Updated 2 years ago
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 5 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆26Updated 2 years ago
• quevedor2 / aneuploidy_score
  R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…
  ☆16Updated 4 years ago
• crazyhottommy / scCustomize
  Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆16Updated 3 years ago
• bioinfo-biols / Code_for_circSC
  Analysis pipeline for our circSC manuscript
  ☆12Updated 2 years ago
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated 2 months ago
• gxiaolab / REDITs
  RNA editing tests
  ☆16Updated 4 years ago
• PoolLab / ReferenceEnhancer
  ☆20Updated last year
• TobiTekath / DTUrtle
  Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
  ☆20Updated 11 months ago
• rnabioco / djvdj
  An R package to analyze single-cell V(D)J data
  ☆24Updated last year
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆23Updated 2 years ago
• henssenlab / TreeShapedRearrangements
  Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)
  ☆15Updated 4 years ago
• navinlabcode / ACT_paper
  Scripts used for the ACT paper
  ☆12Updated 3 years ago
• wenweixiong / MARVEL
  ☆45Updated 7 months ago
• Niinleslie / MesKit
  A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations
  ☆35Updated 3 years ago
• aet21 / EpiSCORE
  Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
  ☆30Updated last year
• Aufiero / circRNAprofiler
  ☆10Updated 4 months ago
• YeoLab / Expedition
  Expedition suite for computing, visualizing, and analyzing single-cell alternative splicing data
  ☆11Updated 7 years ago