Alternatives and similar repositories for TCGAbiolinks

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

• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆331Updated this week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆297Updated 2 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆505Updated 2 weeks ago
• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆477Updated 3 months ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆226Updated 3 years ago
• cole-trapnell-lab / monocle-release
  ☆289Updated 3 years ago
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆418Updated last week
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆421Updated last month
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆348Updated 10 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆304Updated 5 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆293Updated 2 years ago
• cole-trapnell-lab / monocle3
  ☆410Updated 3 weeks ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆202Updated last year
• YuLab-SMU / enrichplot
  Visualization of Functional Enrichment Result
  ☆248Updated 3 weeks ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆223Updated 2 weeks ago
• YuLab-SMU / ChIPseeker
  ChIP peak Annotation, Comparison and Visualization
  ☆239Updated 5 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆350Updated last week
• immunomind / immunarch
  🧬 immunarch [R package] – Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design
  ☆327Updated last month
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆319Updated 2 years ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆436Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆431Updated 7 months ago
• bioFAM / MOFA
  Multi-Omics Factor Analysis
  ☆249Updated 5 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆195Updated 2 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆286Updated last year
• hbctraining / Training-modules
  Materials for short, half-day workshops
  ☆338Updated 3 weeks ago
• IanevskiAleksandr / sc-type
  ☆274Updated 11 months ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆265Updated 10 months ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆314Updated 2 years ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆644Updated 8 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆238Updated 5 months ago