Alternatives and similar repositories for pipelines

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

• wenweixiong / MARVEL
  ☆51Updated last year
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆31Updated 2 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆44Updated 4 years ago
• aet21 / EpiSCORE
  Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
  ☆34Updated 6 months ago
• ajitjohnson / imsig
  Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
  ☆27Updated 4 years ago
• lusystemsbio / NetAct
  Network construction Algorithm
  ☆22Updated last year
• gxiaolab / scAllele
  ☆39Updated last month
• cole-trapnell-lab / pseudospace
  ☆12Updated 6 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated 2 years ago
• secrierlab / EMT
  This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.
  ☆13Updated 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…
  ☆24Updated 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 3 years ago
• dbrg77 / ISSAAC-seq
  ☆18Updated 2 years ago
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆25Updated 2 years ago
• kkdey / GSSG
  Gene Set + S2G strategy annotations analyzed for disease architecture
  ☆55Updated 2 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
• GreenleafLab / ChrAccR
  Analyzing chromatin accessibility data in R
  ☆18Updated 2 years ago
• yizhak-lab-ccg / RNA_MUTECt_WMN
  ☆25Updated 3 years ago
• amcdavid / CellaRepertorium
  Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
  ☆15Updated 3 months ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 9 months ago
• single-cell-genetics / singlecell_neuroseq_paper
  Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  ☆21Updated last year
• immunogenomics / scHLApers
  Code to run the scHLApers pipeline for personalized single-cell HLA quantification
  ☆17Updated last year
• Simon-Leonard / FlexDotPlot
  R package for Flexible dot plots
  ☆29Updated 3 years ago
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 5 years ago
• bjstewart1 / kidney_sc_immune
  Repository for scRNAseq study of human kidneys
  ☆15Updated 6 years ago
• TianLab-Bioinfo / scMAGIC
  A robust and accurate cell type classifier for single cell RNA-seq data
  ☆17Updated 2 years ago
• karthikj89 / scgenetics
  identifying disease critical cell types and programs from single cell RNAseq
  ☆57Updated 3 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• saezlab / footprints
  Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"
  ☆20Updated 7 years ago
• BradBalderson / Cytocipher
  Analysis methods for analysing single cell RNA-seq data; particularly with the goal of checking if tentative clusters of cells are signif…
  ☆38Updated 2 years ago