Alternatives and similar repositories for seqspec:

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

• BUStools / bustools
  Tools for working with BUS files
  ☆93Updated 3 months ago
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆32Updated last month
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆109Updated 2 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆95Updated 2 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…
  ☆114Updated last year
• sheynkman-lab / Long-Read-Proteogenomics
  A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
  ☆42Updated 2 years ago
• nf-core / scdownstream
  A single cell transcriptomics pipeline for QC, integration and making the data presentable
  ☆45Updated this week
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆107Updated last month
• vanallenlab / comut
  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
  ☆91Updated 5 months ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆107Updated last week
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆72Updated this week
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆64Updated 11 months ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated 3 weeks ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆154Updated 3 months ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆72Updated 3 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆58Updated 10 months ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years 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
• snakemake-workflows / rna-seq-kallisto-sleuth
  A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
  ☆66Updated this week
• phageghost / python-genome-browser
  Tools for making plots of genomic datasets in a genome-browser-like format
  ☆31Updated last month
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆122Updated 5 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆117Updated 2 years ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆58Updated last year
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆32Updated 2 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆79Updated 11 months ago
• epi2me-labs / wf-single-cell
  ☆79Updated last week
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 2 months ago
• saezlab / transcriptutorial
  This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
  ☆55Updated last year