Alternatives and similar repositories for SparK

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

• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated last year
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆127Updated 3 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆119Updated last month
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆60Updated 2 years ago
• 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…
  ☆76Updated 2 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
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆67Updated 6 years ago
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆68Updated 3 months ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆29Updated last week
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆117Updated last week
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆49Updated 6 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆82Updated 9 months ago
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆91Updated 3 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆76Updated last year
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆39Updated last week
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆110Updated 4 years ago
• Xinglab / espresso
  ☆63Updated last month
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 4 years ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆173Updated last year
• ivanek / Gviz
  This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
  ☆88Updated 9 months ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆61Updated 2 years ago
• 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
• epi2me-labs / wf-single-cell
  ☆97Updated 3 weeks ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆105Updated 4 years ago
• jianhong / trackViewer
  A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
  ☆74Updated last week
• nloyfer / UXM_deconv
  ☆49Updated 2 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆72Updated 10 months ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆58Updated 4 years ago