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
  ☆100Updated 7 months ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆124Updated 2 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆114Updated 4 months ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆163Updated 7 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…
  ☆86Updated 2 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 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…
  ☆73Updated 2 years ago
• nf-core / cutandrun
  Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream …
  ☆92Updated 3 weeks ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆70Updated 5 months ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• parklab / ShatterSeek
  ☆69Updated last year
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆58Updated 3 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆87Updated 9 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆110Updated 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
  ☆109Updated 4 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆71Updated last year
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆68Updated 3 years ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆113Updated this week
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆192Updated 2 years ago
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆100Updated 7 months ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆102Updated 2 years ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆35Updated 2 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆27Updated 4 months ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆81Updated 5 months ago
• tavareshugo / tutorial_DESeq2_contrasts
  ☆62Updated last year