Alternatives and similar repositories for cis-x:

Users that are interested in cis-x are comparing it to the libraries listed below

• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆34Updated 4 months ago
• PoisonAlien / somaticfreq
  knowledge-based genotyping of cancer hotspots from the tumor BAM files
  ☆21Updated 3 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• AmpliconSuite / AmpliconReconstructorOM
  Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
  ☆17Updated last year
• oicr-gsi / sequenza
  Workflow for Sequenza, cellularity and ploidy
  ☆18Updated 2 weeks ago
• vanallenlab / facets
  Implementation of FACETS for Terra
  ☆12Updated 2 years ago
• homeveg / nuctools
  software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data
  ☆17Updated 5 years ago
• Cibiv / trumicount
  Correctly counting molecules using unique molecular identifiers (UMIs)
  ☆9Updated 3 years ago
• skandlab / SMuRF
  ☆22Updated 2 months ago
• 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…
  ☆16Updated last year
• VanLoo-lab / gritic
  A tool for timing complex copy number gains in cancer.
  ☆17Updated 3 weeks ago
• AlexandrovLab / EnsembleVariantCallingPipeline
  The EnsembleVariantCallingPipeline takes files in FASTQ or BAM format and performs SNV and INDEL variant calling from 4 variant callers (…
  ☆13Updated last year
• smshuai / DriverPower
  DriverPower
  ☆26Updated 2 months ago
• parklab / MSIprofiler
  Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data
  ☆20Updated 11 months ago
• AlexandrovLab / SigProfilerTopography
  SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…
  ☆19Updated last month
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• vanallenlab / MutPanningV2
  This repository contains the source code of the revised version of MutPanning. MutPanning is publicly available under the BSD3-Clause ope…
  ☆12Updated 5 years ago
• mandricigor / imrep
  ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
  ☆28Updated 5 years ago
• califano-lab / OncoSig
  Code to run OncoSig Analyses
  ☆18Updated 4 years ago
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆35Updated 7 years ago
• ICGC-TCGA-PanCancer / Seqware-BWA-Workflow
  This is the BWA workflow used in the PanCancer project used to allign all the BAM files.
  ☆11Updated 2 years ago
• raphael-group / calder
  CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …
  ☆15Updated last year
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 3 weeks ago
• amf71 / ECLIPSE
  ☆11Updated last year
• KChen-lab / Texomer
  Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
  ☆20Updated 4 years ago
• shahcompbio / timescape
  Visualization tool for temporal clonal evolution.
  ☆17Updated 5 years ago
• slagtermaarten / LOHHLA
  Fork of https://bitbucket.org/mcgranahanlab/lohhla
  ☆17Updated 5 years ago
• beroukhim-lab / BISCUT-py3
  ☆12Updated 11 months ago
• jiujiezz / tsnad
  Detecting somatic mutations and predicting tumor-specific neo-antigens
  ☆28Updated 3 years ago
• mskilab-org / dryclean
  Irons out wrinkles in noisy coverage data using robust PCA
  ☆13Updated this week