Alternatives and similar repositories for JaBbA

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

• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated 2 weeks ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆97Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 7 months ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated 2 months ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆50Updated 2 years ago
• huishenlab / biscuit
  BISulfite-seq CUI Toolkit
  ☆24Updated 3 weeks ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆76Updated 5 months ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆61Updated 4 months ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆54Updated 4 months ago
• FusionInspector / FusionInspector
  FusionInspector code
  ☆58Updated 3 weeks ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆80Updated last week
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 11 months ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated last year
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆52Updated 3 years ago
• wososa / PSI-Sigma
  PSI-Sigma
  ☆38Updated last year
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆43Updated last week
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆33Updated 10 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated last year
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 3 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated last month
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 3 years ago
• Oshlack / JAFFA
  JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
  ☆101Updated 4 months ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆91Updated 3 months ago
• ncbi / BAMscale
  BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …
  ☆72Updated 10 months ago
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆67Updated 3 weeks ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆63Updated 11 months ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago