Transcript quantification import for modular pipelines
☆142Sep 30, 2025Updated 5 months ago
Alternatives and similar repositories for tximport
Users that are interested in tximport are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Modeling and correcting fragment sequence bias for RNA-seq☆24Jun 4, 2024Updated last year
- Transcript quantification import with automatic metadata detection☆70Mar 3, 2026Updated 3 weeks ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- Fast fusion detection using kallisto☆79Jun 11, 2025Updated 9 months ago
- Computable build reports, package metadata, and download stats from the Bioconductor project☆22Mar 13, 2026Updated last week
- A Grammar of Data Manipulation for Omics Data☆21Aug 31, 2020Updated 5 years ago
- Near-optimal RNA-Seq quantification☆753Mar 16, 2026Updated last week
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆870Mar 11, 2026Updated last week
- Interactive benchmarking of ranking and assignment methods☆16Dec 13, 2025Updated 3 months ago
- Simple pure Python SAM parser and objects for working with SAM records☆64Updated this week
- Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes☆31Jun 16, 2024Updated last year
- Differential analysis of RNA-Seq☆312May 28, 2025Updated 9 months ago
- Prepare Sailfish and Salmon output for downstream analysis☆42Jun 6, 2019Updated 6 years ago
- Workflow for ZINB-WaVE + DESeq2 intergration for single-cell RNA-seq☆30Jan 6, 2021Updated 5 years ago
- Explore design matrices interactively with R/Shiny☆38Mar 16, 2026Updated last week
- Response to blog post about Salmon☆37Sep 3, 2017Updated 8 years ago
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 6 months ago
- Glimma R package☆50Sep 2, 2024Updated last year
- Tools for processing UMI RNA-tag data☆131Mar 15, 2023Updated 3 years ago
- Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data☆167Oct 2, 2025Updated 5 months ago
- ☆57Aug 11, 2022Updated 3 years ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆26Dec 11, 2017Updated 8 years ago
- Exposing public genomics data via computable and searchable metadata☆13Jul 9, 2024Updated last year
- Using kallisto for metagenomic analysis☆49Jan 12, 2017Updated 9 years ago
- A grammar of genomic data transformation☆154Updated this week
- R data package for annotating/converting Gene IDs☆169Jul 6, 2025Updated 8 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 7 months ago
- Draw heatmap simply using a tidy data frame☆358Feb 7, 2026Updated last month
- ☆96Apr 18, 2024Updated last year
- Preprocessing of single-cell RNA-Seq (deprecated)☆62Jul 5, 2019Updated 6 years ago
- Useful tools for working with Salmon output☆38Jun 24, 2020Updated 5 years ago
- Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.☆11Oct 8, 2021Updated 4 years ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆252Jan 10, 2026Updated 2 months ago
- Abbreviate strings to short, unique identifiers☆24May 10, 2022Updated 3 years ago
- An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..☆821Aug 4, 2024Updated last year
- Simplify functional enrichment results☆124Jan 30, 2026Updated last month
- Visualization of Functional Enrichment Result☆257Mar 2, 2026Updated 3 weeks ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆51Apr 9, 2021Updated 4 years ago
- Bioconductor cheat sheet☆191Aug 26, 2024Updated last year