Alternatives and similar repositories for spladder

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

• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆108Updated 4 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆113Updated 4 years ago
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆151Updated 3 months ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆115Updated last month
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆136Updated last year
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆73Updated last month
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• jernst98 / ChromHMM
  ☆90Updated 4 months ago
• AAlhendi1707 / countToFPKM
  Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
  ☆63Updated 4 years ago
• nloyfer / meth_atlas
  ☆51Updated 3 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆111Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated last month
• broadinstitute / PhylogicNDT
  ☆80Updated 7 months ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆82Updated 9 months ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated last year
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆77Updated 2 years ago
• nloyfer / UXM_deconv
  ☆49Updated 2 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆133Updated last year
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated 2 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 7 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆60Updated last month
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆81Updated 4 years ago