Alternatives and similar repositories for TCGAbiolinks:

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

• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆460Updated 4 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆481Updated 2 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆270Updated 5 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆559Updated 4 months ago
• cole-trapnell-lab / monocle3
  ☆373Updated 2 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆325Updated 4 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆449Updated last week
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆317Updated this week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆525Updated last month
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆328Updated this week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆601Updated last month
• YuLab-SMU / enrichplot
  Visualization of Functional Enrichment Result
  ☆241Updated 2 weeks ago
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆395Updated last week
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆290Updated 4 years ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆388Updated 2 weeks ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆274Updated last month
• cole-trapnell-lab / monocle-release
  ☆284Updated 2 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆194Updated 10 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆407Updated last month
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆408Updated 2 months ago
• hbctraining / Intro-to-DGE
  ☆192Updated last week
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆465Updated 10 months ago
• IOBR / IOBR
  IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.
  ☆234Updated 2 weeks ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆268Updated 3 weeks ago
• navinlabcode / copykat
  ☆228Updated 9 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆368Updated 3 months ago
• YuLab-SMU / ChIPseeker
  ChIP peak Annotation, Comparison and Visualization
  ☆234Updated last month
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆205Updated this week
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆221Updated 2 years ago