HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
☆129Apr 12, 2020Updated 5 years ago
Alternatives and similar repositories for htseq
Users that are interested in htseq are comparing it to the libraries listed below
Sorting:
- HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.☆107Feb 4, 2026Updated last month
- Processing and analysis of data coming from Illumina sequencing machines☆10Updated this week
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆870Mar 11, 2026Updated last week
- GFF and GTF file manipulation and interconversion☆314Jan 26, 2026Updated last month
- RNA-seq aligner☆2,158Mar 18, 2025Updated last year
- Graph-based alignment (Hierarchical Graph FM index)☆530Jan 27, 2026Updated last month
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆329Mar 16, 2025Updated last year
- pyAffy: Processing raw data from Affymetrix expression microarrays in Python.☆18Dec 6, 2016Updated 9 years ago
- A deletion finder through re-aligning the whole soft-clipping read☆12Jul 2, 2016Updated 9 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆463Updated this week
- GenomeTools: Scripts and Classes for Working with Genomic Data☆12Jun 7, 2018Updated 7 years ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆722Updated this week
- A software for the multispecies design of CRISPR/Cas9 libraries☆36Oct 7, 2022Updated 3 years ago
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 10 months ago
- Performant Pythonic GenomicRanges☆494Jan 27, 2026Updated last month
- ☆13Jan 8, 2020Updated 6 years ago
- MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation☆139Dec 15, 2022Updated 3 years ago
- Oxford Nanopore HDF/Fast5 to CRAM conversion tool☆22Dec 30, 2019Updated 6 years ago
- Near-optimal RNA-Seq quantification☆750Mar 10, 2026Updated last week
- Peakzilla is a self-learning algorithm to identify transcription factor binding sites from ChIP-seq data. I would be very happy if you tr…☆21Aug 18, 2025Updated 7 months ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆213May 14, 2020Updated 5 years ago
- MUltiScale enrIchment Calling for ChIP-Seq Datasets☆23Mar 14, 2019Updated 7 years ago
- Python module and utility programs for working with GFF files☆33Nov 25, 2020Updated 5 years ago
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆195Mar 1, 2026Updated 2 weeks ago
- A quality control analysis tool for high throughput sequencing data☆587Jan 5, 2026Updated 2 months ago
- Tools for working with BUS files☆102May 27, 2025Updated 9 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆267Updated this week
- FREE Divergence Error-Correcting DNA Barcodes☆10Jun 23, 2018Updated 7 years ago
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,054Feb 4, 2026Updated last month
- ☆13Sep 4, 2025Updated 6 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,027Mar 11, 2025Updated last year
- Code for differential splicing comparison paper (Soneson, Matthes, et al.)☆20Jun 23, 2016Updated 9 years ago
- ☆320Mar 31, 2020Updated 5 years ago
- TreeGrafter is a new software tool for annotating uncharacterized protein sequences, using annotated phylogenetic trees.☆13Mar 12, 2026Updated last week
- ☆12Jan 21, 2016Updated 10 years ago
- Kart: A divide-and-conquer algorithm for NGS read mapping with high error tolerance☆26May 21, 2020Updated 5 years ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,429Mar 12, 2026Updated last week
- Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R☆32Feb 23, 2026Updated 3 weeks ago
- Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…☆883Updated this week