Alternatives and similar repositories for TCGAWorkflow

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

• icbi-lab / Immunophenogram
  ☆41Updated 7 years ago
• icbi-lab / immune_deconvolution_benchmark
  Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…
  ☆44Updated 5 years ago
• waldronlab / HGNChelper
  Identify and correct invalid gene symbols
  ☆61Updated last year
• XSLiuLab / tumor-immunogenicity-score
  TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
  ☆33Updated 4 years ago
• foreverdream2 / dysfunction_interaction_test
  ☆30Updated 7 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆46Updated 2 years ago
• greenelab / RNAseq_titration_results
  Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
  ☆37Updated 2 years ago
• GfellerLab / EPIC
  Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
  ☆83Updated 2 years ago
• waldronlab / MultiAssayWorkshop
  Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
  ☆24Updated 6 months ago
• lagelab / quack
  Machine learning algorithm to predict biological pathway relationships based on functional genomics networks
  ☆20Updated 7 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated last year
• riazn / bms038_analysis
  Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for man…
  ☆52Updated 7 years ago
• ebecht / MCPcounter
  ☆59Updated 3 years ago
• montilab / hypeR
  An R Package for Geneset Enrichment Workflows
  ☆76Updated last month
• combiz / scFlow
  Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
  ☆57Updated last year
• uc-bd2k / GREIN
  GREIN : GEO RNA-seq Experiments Interactive Navigator
  ☆50Updated 6 years ago
• Gibbsdavidl / Immune-Subtype-Clustering
  This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".
  ☆18Updated 6 years ago
• SamBuckberry / RUN-WGCNA
  Wrapper R scripts for performing a weighted-gene co-expression network analysis (WGCNA)
  ☆30Updated 10 years ago
• crazyhottommy / scRNA-seq-workshop-Fall-2019
  Harvard FAS informatics scRNAseq workshop website
  ☆38Updated 6 years ago
• chunjie-sam-liu / GSCALite
  GSCALite: Gene set for cancer analysis
  ☆23Updated 3 years ago
• bigbioinformatics / single_cell_rna_seq_workshop
  repository for the single cell RNA-Seq workshop
  ☆31Updated 4 years ago
• wuaipinglab / ImmuCC
  Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
  ☆26Updated 4 years ago
• hammerlab / multi-omic-urothelial-anti-pdl1
  Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis
  ☆24Updated 8 years ago
• caravagnalab / revolver
  Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
  ☆66Updated 3 years ago
• DavisLaboratory / singscore
  An R/Bioconductor package that implements a single-sample molecular phenotyping approach
  ☆46Updated 3 months ago
• mikegloudemans / gwas-download
  Easily download publicly available GWAS summary statistics.
  ☆78Updated 2 years ago
• PCAWG-11 / Evolution
  Code accompanying The Evolutionary history of 2,658 cancers
  ☆46Updated 4 years ago
• fpbarthel / GLASS
  GLASS consortium
  ☆42Updated 5 years ago
• jokergoo / cola
  A General Framework for Consensus Partitioning
  ☆65Updated 11 months ago