Alternatives and similar repositories for seqspec

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

• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆122Updated last month
• BUStools / bustools
  Tools for working with BUS files
  ☆102Updated 5 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆115Updated last month
• nf-core / scdownstream
  A single cell transcriptomics pipeline for QC, integration and making the data presentable
  ☆78Updated last week
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆119Updated last month
• skrakau / PureCLIP
  Capturing protein-RNA interaction footprints from single-nucleotide CLIP-seq data
  ☆31Updated 4 years ago
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆45Updated 2 months ago
• vanallenlab / comut
  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
  ☆96Updated last year
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆117Updated last week
• tavareshugo / tutorial_DESeq2_contrasts
  ☆63Updated last year
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆127Updated 3 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆76Updated last year
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆113Updated last week
• epi2me-labs / wf-single-cell
  ☆97Updated 3 weeks ago
• nf-core / airrflow
  B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
  ☆69Updated last week
• 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 …
  ☆104Updated 3 weeks ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆58Updated 4 years ago
• mckennalab / FlashFry
  FlashFry: The rapid CRISPR target site characterization tool
  ☆77Updated last year
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆39Updated last week
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆74Updated last year
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆84Updated this week
• mdozmorov / ChIP-seq_notes
  Notes on ChIP-seq and other-seq-related tools
  ☆26Updated 3 months ago
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆100Updated 11 months 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
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 5 months ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆72Updated 10 months ago
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆84Updated last year
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆82Updated 9 months ago