RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
☆461Feb 28, 2026Updated this week
Alternatives and similar repositories for RSEM
Users that are interested in RSEM are comparing it to the libraries listed below
Sorting:
- RNA-seq aligner☆2,146Mar 18, 2025Updated 11 months ago
- A short tutorial on how to use RSEM☆138Apr 19, 2020Updated 5 years ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆862May 29, 2024Updated last year
- Cutadapt removes adapter sequences from sequencing reads☆572Jan 12, 2026Updated last month
- Near-optimal RNA-Seq quantification☆724Updated this week
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆462Dec 26, 2024Updated last year
- Transcript assembly and quantification for RNA-Seq☆489Dec 26, 2025Updated 2 months ago
- Trinity RNA-Seq de novo transcriptome assembly☆883Feb 7, 2025Updated last year
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,425Updated this week
- Graph-based alignment (Hierarchical Graph FM index)☆530Jan 27, 2026Updated last month
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,053Feb 4, 2026Updated 3 weeks ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆541Feb 24, 2026Updated last week
- MACS -- Model-based Analysis of ChIP-Seq☆767Updated this week
- BEDOPS: high-performance genomic feature operations☆360Apr 29, 2025Updated 10 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆262Jul 12, 2025Updated 7 months ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,292Jan 22, 2026Updated last month
- bedtools - the swiss army knife for genome arithmetic☆1,025Mar 11, 2025Updated 11 months ago
- TransDecoder source☆301Sep 29, 2025Updated 5 months ago
- Tools for handling Unique Molecular Identifiers in NGS data sets☆537Feb 2, 2026Updated last month
- ☆320Mar 31, 2020Updated 5 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,128Feb 13, 2026Updated 2 weeks ago
- Tools to process and analyze deep sequencing data.☆751Jul 23, 2025Updated 7 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,528Jun 1, 2025Updated 9 months ago
- SRA Tools☆1,309Updated this week
- Strelka2 germline and somatic small variant caller☆390Dec 29, 2021Updated 4 years ago
- Rapid Mapping-based Isoform Quantification from RNA-Seq Reads☆127Jun 9, 2022Updated 3 years ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,707Mar 22, 2025Updated 11 months ago
- SUPPA: Fast quantification of splicing and differential splicing☆293Nov 6, 2025Updated 3 months ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,849Feb 24, 2026Updated last week
- GFF and GTF file manipulation and interconversion☆314Jan 26, 2026Updated last month
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,520Updated this week
- The next version of bwa-mem☆819Oct 15, 2025Updated 4 months ago
- Differential analysis of RNA-Seq☆312May 28, 2025Updated 9 months ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation☆137Dec 15, 2022Updated 3 years ago
- Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.☆148Aug 30, 2021Updated 4 years ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆864Feb 8, 2026Updated 3 weeks ago
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆445Aug 8, 2025Updated 6 months ago
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆293Dec 17, 2025Updated 2 months ago