Alternatives and similar repositories for SEACR

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

• 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 …
  ☆106Updated last month
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆198Updated 2 years ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆175Updated last year
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆139Updated 5 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆128Updated 3 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆193Updated 3 months ago
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated last month
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆146Updated 2 years ago
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆126Updated last week
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆92Updated 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.
  ☆105Updated 3 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆117Updated 3 months ago
• epi2me-labs / wf-single-cell
  ☆102Updated last month
• harvardinformatics / ATAC-seq
  ☆145Updated 7 years ago
• Xinglab / rmats2sashimiplot
  ☆157Updated 7 months ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆220Updated last month
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆109Updated 11 months ago
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆151Updated last year
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆156Updated last year
• tavareshugo / tutorial_DESeq2_contrasts
  ☆63Updated last year
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArc…
  ☆76Updated last week
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆121Updated last year
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆178Updated 3 weeks ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆88Updated 5 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆185Updated last year