Alternatives and similar repositories for seqspec:

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

• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• BUStools / bustools
  Tools for working with BUS files
  ☆93Updated 4 months ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆35Updated 2 months ago
• vanallenlab / comut
  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
  ☆91Updated 7 months ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆100Updated 3 months ago
• nf-core / scdownstream
  A single cell transcriptomics pipeline for QC, integration and making the data presentable
  ☆47Updated last month
• sheynkman-lab / Long-Read-Proteogenomics
  A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
  ☆43Updated 2 years ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆57Updated 2 weeks ago
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆101Updated 2 years ago
• PierreBSC / Viral-Track
  ☆57Updated 4 years ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆108Updated last month
• skrakau / PureCLIP
  Capturing protein-RNA interaction footprints from single-nucleotide CLIP-seq data
  ☆29Updated 3 years ago
• tavareshugo / tutorial_DESeq2_contrasts
  ☆58Updated 9 months ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆115Updated last year
• 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 …
  ☆87Updated last month
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated last month
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆154Updated 4 months ago
• snakemake-workflows / rna-seq-kallisto-sleuth
  A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
  ☆67Updated this week
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆64Updated last year
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆60Updated 3 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆67Updated last year
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆108Updated last month
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆32Updated 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…
  ☆73Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆117Updated 2 years ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆78Updated 4 months ago