Alternatives and similar repositories for machina

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

• broadinstitute / PhylogicNDT
  ☆79Updated 6 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆64Updated 4 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• icbi-lab / nextNEOpi
  nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
  ☆78Updated 5 months ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• broadinstitute / RNA_MUTECT_1.0-1
  ☆39Updated 5 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆72Updated 2 weeks ago
• PCAWG-11 / Evolution
  Code accompanying The Evolutionary history of 2,658 cancers
  ☆46Updated 4 years ago
• gxiaolab / REDITs
  RNA editing tests
  ☆17Updated 5 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆81Updated 3 years ago
• ding-lab / PanCanAtlasGermline
  ☆44Updated 7 years ago
• 10XGenomics / bamtofastq
  Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
  ☆66Updated last week
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆44Updated 4 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆30Updated 7 months ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆42Updated 4 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• fpbarthel / GLASS
  GLASS consortium
  ☆42Updated 5 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆55Updated last year
• JunyueC / sci-RNA-seq3_pipeline
  Processing pipeline scripts for sci-RNA-seq3 (bash, R, python)
  ☆43Updated 4 years ago
• nghiavtr / SCmut
  ☆34Updated 6 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• 10XGenomics / scHLAcount
  Count HLA alleles in single-cell RNA-seq data
  ☆62Updated 4 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• HorvathLab / NGS
  Next-Gen Sequencing tools from the Horvath Lab
  ☆44Updated last month
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• cboix / EPIMAP_ANALYSIS
  Epimap processing and analysis code repository
  ☆33Updated 3 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 3 years ago
• cole-trapnell-lab / cicero-release
  ☆58Updated last year