Alternatives and similar repositories for pipelines

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

• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• GreenleafLab / ChrAccR
  Analyzing chromatin accessibility data in R
  ☆18Updated 2 years ago
• wenweixiong / MARVEL
  ☆49Updated last year
• secrierlab / EMT
  This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.
  ☆13Updated 2 years ago
• WRui / Post_Implantation
  ☆27Updated 4 years ago
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• gxiaolab / scAllele
  ☆37Updated last year
• aet21 / EpiSCORE
  Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
  ☆33Updated 4 months ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆30Updated 2 years ago
• franklinhuanglab / scRNA-seq-Analysis-of-Prostate-Cancer-Samples
  Code for the manuscript "Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial c…
  ☆23Updated 3 years ago
• bsml320 / scGWAS
  A method which leverages scRNA-seq data to achieve two goals: (1) to infer the cell types in which the disease-associated genes manifest …
  ☆26Updated 2 years ago
• ajitjohnson / imsig
  Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
  ☆27Updated 4 years ago
• kkdey / GSSG
  Gene Set + S2G strategy annotations analyzed for disease architecture
  ☆53Updated 2 years ago
• cole-trapnell-lab / pseudospace
  ☆12Updated 5 years ago
• Henikoff / scCUT-Tag
  ☆17Updated 2 years ago
• immunogenomics / scHLApers
  Code to run the scHLApers pipeline for personalized single-cell HLA quantification
  ☆17Updated last year
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• single-cell-genetics / singlecell_neuroseq_paper
  Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  ☆21Updated last year
• YiPeng-Gao / scDaPars
  Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
  ☆17Updated 4 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated last year
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• neurorestore / DE-analysis
  ☆39Updated 4 years ago
• saezlab / footprints
  Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"
  ☆20Updated 7 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• Simon-Leonard / FlexDotPlot
  R package for Flexible dot plots
  ☆29Updated 3 years ago
• shendurelab / single-cell-ko-screens
  Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hi…
  ☆26Updated 3 years ago
• UPSUTER / GEMLI
  ☆32Updated 6 months ago
• lusystemsbio / NetAct
  Network construction Algorithm
  ☆22Updated 11 months ago
• cole-trapnell-lab / monocle2-rge-paper
  Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)
  ☆29Updated 5 years ago
• bioinfo-biols / Code_for_circSC
  Analysis pipeline for our circSC manuscript
  ☆13Updated 3 years ago