Alternatives and similar repositories for lichee:

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

• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• jrflab / modules
  MSKCC Reis-Filho Lab pipeline thingy
  ☆17Updated 9 months ago
• sigven / cacao
  Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
  ☆21Updated 4 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 2 months ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 3 months ago
• d3b-center / annoFuse
  Filter and prioritize fusion calls
  ☆20Updated 7 months ago
• eyzhao / hrdetect-pipeline
  ☆34Updated 5 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆19Updated 3 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 6 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 2 months ago
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆27Updated 2 years ago
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated 4 months ago
• QingliGuo / FFPEsig
  Codes and Data for FFPEsig manuscript
  ☆16Updated last year
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆37Updated 4 years ago
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆23Updated 3 years ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆29Updated 9 months ago
• caravagnalab / CNAqc
  CNAqc - Copy Number Alteration (CNA) Quality Check package
  ☆21Updated 2 months ago
• jmw86069 / splicejam
  Sashimi plots for RNA-seq data using detected transcripts
  ☆28Updated last month
• shahcompbio / timescape
  Visualization tool for temporal clonal evolution.
  ☆17Updated 5 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated last month
• mskilab-org / dryclean
  Irons out wrinkles in noisy coverage data using robust PCA
  ☆14Updated 2 weeks ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆22Updated last year
• morrislab / pairtree
  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…
  ☆37Updated last year
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago