☆321Mar 31, 2020Updated 6 years ago
Alternatives and similar repositories for cufflinks
Users that are interested in cufflinks are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Spliced read mapper for RNA-Seq☆92Jul 9, 2023Updated 2 years ago
- Near-optimal RNA-Seq quantification☆756Mar 16, 2026Updated last month
- RNA-seq aligner☆2,178Mar 18, 2025Updated last year
- Transcript assembly and quantification for RNA-Seq☆502Dec 26, 2025Updated 3 months ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆470Apr 7, 2026Updated last week
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆471Apr 10, 2026Updated last week
- Spliced read mapper for RNA-Seq☆22May 24, 2018Updated 7 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆532Jan 27, 2026Updated 2 months ago
- A fast and sensitive gapped read aligner☆787Mar 7, 2026Updated last month
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,877Apr 11, 2026Updated last week
- Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter☆19Feb 20, 2018Updated 8 years ago
- bedtools - the swiss army knife for genome arithmetic☆1,027Mar 11, 2025Updated last year
- Trinity RNA-Seq de novo transcriptome assembly☆888Feb 7, 2025Updated last year
- Rapid Mapping-based Isoform Quantification from RNA-Seq Reads☆127Jun 9, 2022Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Analysis from kallisto paper☆32Feb 10, 2016Updated 10 years ago
- An ultrafast memory-efficient short read aligner☆267May 11, 2022Updated 3 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.☆1,062Mar 24, 2026Updated 3 weeks ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆269Mar 15, 2026Updated last month
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆876Mar 11, 2026Updated last month
- Cutadapt removes adapter sequences from sequencing reads☆576Apr 6, 2026Updated last week
- STAR-Fusion codebase☆250Oct 4, 2025Updated 6 months ago
- FASTA/FASTQ pre-processing programs☆200Mar 4, 2022Updated 4 years ago
- Tools for working with SAM/BAM data☆609Dec 22, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,730Mar 22, 2025Updated last year
- ☆89Nov 11, 2020Updated 5 years ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,439Apr 9, 2026Updated last week
- Differential analysis of RNA-Seq☆312May 28, 2025Updated 10 months ago
- Mummer alignment tool☆554Feb 4, 2025Updated last year
- MACS -- Model-based Analysis of ChIP-Seq☆772Apr 8, 2026Updated last week
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆727Updated this week
- Official code repository for GATK versions 4 and up☆1,933Apr 10, 2026Updated last week
- Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…☆1,420May 31, 2023Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Tools for working with BUS files☆102May 27, 2025Updated 10 months ago
- Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.☆148Aug 30, 2021Updated 4 years ago
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆235Feb 17, 2022Updated 4 years ago
- BEDOPS: high-performance genomic feature operations☆365Apr 29, 2025Updated 11 months ago
- Tool for the detection and quantification of alternative splicing events from RNA-Seq data.☆111Jul 23, 2025Updated 8 months ago
- C library for high-throughput sequencing data formats☆915Updated this week
- Next generation sequencing reads de novo assembler.☆239Sep 20, 2025Updated 6 months ago