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salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignmentalevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.pufferfish
An efficient index for the colored, compacted, de Bruijn graphRapMap
Rapid sensitive and accurate read mapping via quasi-mappingcuttlefish
Building the compacted de Bruijn graph efficiently from references or reads.oarfish
long read RNA-seq quantificationterminus
kmers
A bit-packed k-mer representation (and relevant utilities) for rustsimpleaf
A rust framework to make using alevin-fry even simplerwasabi
Prepare Sailfish and Salmon output for downstream analysisSalmonTools
Useful tools for working with Salmon outputRapClust
Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classespiscem
Rust wrapper for the next generation (still currently in C++)shoal
Improved multi-sample transcript abundance estimates using adaptive priorsgrangers
pufferfish2
EDS
💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage formatpyroe
grouper
piscem-infer
mazu
A Rust library for building modular, fast and compact indexes over genomic datarainbowfish
A succinct colored dBG representationquark
semi-reference-based short read compressionusefulaf
Useful scripts and tools related to alevin-frymeasuresmatter
A treatise on quantification and differential expression from RNA-seq datacombine-lab.github.io
quantaf
seine-rs
A (rust)🦀 library and suite of tools for manipulating and processing the output of salmon, alevin, and alevin-fry 🐟piscem-cpp
A small sparse and fast reference index based on SShash and Tiling encodingsc-census
GRASS
Graph-Regularized Annotation via Semi-Supervised learningTreeTerminus
COMBINE-lab.github.io-OLD
Lab websitematryoshka
Methods for the automated discovery of hierarchically-structured chromatin domainsforseti
pcalib
A small "lightweight" implementation of PCA in C++ using the Eigen libraryperplexity
alevin-paper-pipeline
A simple pipeline using CGAT framework for benchmarking and analysis.seq_geom_xform
A crate to convert "complex" sequence library geometries to "simple" geometriesefgdl-spec
Specification for the extended fragment geometry description languageseqproc
seq_geom_parser
Testing out rust parsing of single-cell library geometry specificationsroe
roers
protocol-estuary
xz
A GitHub clone of the XZ repo (http://git.tukaani.org/xz.git) — not from the original authorLabRules
A list of rules and hints (on various different subjects) for members of the COMBINE lab. Others may also find them useful.txome-clustering
Meaningful and efficient clustering of de novo transcriptome assembly results (better name pending).cqf-rust
An attempt at rustification of the CQF (https://github.com/splatlab/cqf)libgff
splitp
split-seq preprocessingquant-tx-diversity
alevin-fry-paper-scripts
scrna-ambiguity
alevin-tutorial
This is a support website for Alevin-tool (part of Salmon).radicl-cpp
Internal library for basic reading and writing of .rad files in C++14FastaDigest
Get the "signature" of fasta filesrsrs
Reference Signatures (rs) in Rust (rs)libradicl
simplr
KallistoFormatDescription
Documenting the (binary) output format used by Kallistopufferfish_experiments
CSE549-txpCoverage
QuantAnalysis
radtk
Various tools for working with RAD fileslr_quant_benchmarks
A replicable and modular benchmark for long-read RNA transcript quantification methodsLove Open Source and this site? Check out how you can help us