Alternatives and similar repositories for SPONGE

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

• AlexandrovLab / SigProfilerMatrixGeneratorR
  R wrapper for utilizing the SigProfilerMatrixGenerator framework
  ☆20Updated 2 years ago
• PoisonAlien / somaticfreq
  knowledge-based genotyping of cancer hotspots from the tumor BAM files
  ☆21Updated 3 years ago
• caravagnalab / CNAqc
  Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation
  ☆24Updated last month
• MonashBioinformaticsPlatform / celaref
  ☆14Updated 6 years ago
• stephenturner / msigdf
  Molecular Signatures Database (MSigDB) in a data frame
  ☆16Updated 6 years ago
• yasinkaymaz / singleCellRNAseq_workshop
  Introduction to single cell RNAseq data analysis and interpretation course work provided by Harvard Informatics Team.
  ☆16Updated 6 years ago
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 6 years ago
• qingjian1991 / MPTevol
  ☆10Updated 2 years ago
• jokergoo / BioCartaImage
  BioCarta pathway images
  ☆11Updated 2 years ago
• davemcg / awesome_genome_browsers
  ☆10Updated 6 years ago
• BUStools / BUS_notebooks_R
  R vignettes for processing BUS format single-cell RNA-seq files
  ☆21Updated 5 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• taoshengxu / CancerSubtypes
  ☆16Updated 2 years ago
• hanasusak / cDriver
  cDriver R package for finding candidate driver genes in cancers
  ☆18Updated 7 years ago
• stephaniehicks / methylCC
  R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms
  ☆18Updated 3 years ago
• quevedor2 / aneuploidy_score
  R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…
  ☆16Updated 4 years ago
• NourMarzouka / multiclassPairs
  Build single sample pair-based (rule-based) classifiers using top-score pairs or random forest for multi-class problems.
  ☆13Updated 2 years ago
• yigbt / multiGSEA
  The `multiGSEA` R package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers.
  ☆20Updated 2 weeks ago
• beroukhim-lab / BISCUT-py3
  ☆12Updated last year
• crazyhottommy / single-cell-DNAseq-notes
  ☆16Updated 3 years ago
• flemingtonlab / SpliceTools
  ☆17Updated last year
• CompEpigen / ezASCAT
  Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R
  ☆12Updated 3 years ago
• cboix / epimap_vis
  Code for EpiMap data browser
  ☆14Updated last year
• beroukhim-lab / ascets
  This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…
  ☆18Updated last year
• skandlab / MutSpot
  ☆17Updated 2 years ago
• yuewangpanda / BioMethyl
  An R package to interpret biological trends from DNA methylation data
  ☆18Updated 3 years ago
• mikelove / zinbwave-deseq2
  Workflow for ZINB-WaVE + DESeq2 intergration for single-cell RNA-seq
  ☆31Updated 4 years ago
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 4 years ago
• myles-lewis / glmmSeq
  Gene-level general linear mixed model
  ☆23Updated last month
• Terkild / CITE-seq_optimization
  Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
  ☆10Updated 4 years ago