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
  ☆102Updated 8 months ago
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆51Updated last month
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆124Updated 4 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆117Updated 3 months ago
• vanallenlab / comut
  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
  ☆96Updated last year
• epi2me-labs / wf-single-cell
  ☆104Updated 2 weeks ago
• nf-core / airrflow
  B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
  ☆74Updated this week
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆111Updated 3 months ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆123Updated 2 months ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆124Updated this week
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆39Updated 2 weeks ago
• skrakau / PureCLIP
  Capturing protein-RNA interaction footprints from single-nucleotide CLIP-seq data
  ☆32Updated 4 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆73Updated last year
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆82Updated last year
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆128Updated 3 years ago
• nf-core / scdownstream
  A single cell transcriptomics pipeline for QC, integration and making the data presentable
  ☆83Updated this week
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆119Updated 3 years ago
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆110Updated last year
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆74Updated 2 years ago
• jernst98 / ChromHMM
  ☆94Updated 7 months ago
• tavareshugo / tutorial_DESeq2_contrasts
  ☆65Updated last year
• igvteam / igv-notebook
  Module for embedding igv.js in an IPython notebook
  ☆80Updated 11 months ago
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆153Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆74Updated last year
• broadinstitute / pyqtl
  Collection of analysis tools for quantitative trait loci
  ☆61Updated last month
• ernstlab / full_stack_ChromHMM_annotations
  Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
  ☆38Updated last year
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆101Updated last year
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆121Updated last year
• 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…
  ☆78Updated 2 years ago