Discover COMBINE-lab/RapClust Open Source project

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

765

alevin-fry

An efficient index for the colored, compacted, de Bruijn graph

159

pufferfish

107

RapMap

Rapid sensitive and accurate read mapping via quasi-mapping

Building the compacted de Bruijn graph efficiently from references or reads.

cuttlefish

long read RNA-seq quantification

oarfish

terminus

A bit-packed k-mer representation (and relevant utilities) for rust

kmers

A rust framework to make using alevin-fry even simpler

simpleaf

Prepare Sailfish and Salmon output for downstream analysis

wasabi

SalmonTools

Useful tools for working with Salmon output

Rust wrapper for the next generation (still currently in C++)

piscem

Improved multi-sample transcript abundance estimates using adaptive priors

shoal

grangers

pufferfish2

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

EDS

pyroe

grouper

piscem-infer

mazu

A Rust library for building modular, fast and compact indexes over genomic data

A succinct colored dBG representation

rainbowfish

semi-reference-based short read compression

quark

minnow

Useful scripts and tools related to alevin-fry

usefulaf

A treatise on quantification and differential expression from RNA-seq data

measuresmatter

combine-lab.github.io

HTML

quantaf

Nextflow

seine-rs

A (rust)🦀 library and suite of tools for manipulating and processing the output of salmon, alevin, and alevin-fry 🐟

A small sparse and fast reference index based on SShash and Tiling encoding

piscem-cpp

sc-census

GRASS

Graph-Regularized Annotation via Semi-Supervised learning

Methods for the automated discovery of hierarchically-structured chromatin domains

TreeTerminus

COMBINE-lab.github.io-OLD

Lab website

HTML

matryoshka

forseti

A small "lightweight" implementation of PCA in C++ using the Eigen library

pcalib

perplexity

A simple pipeline using CGAT framework for benchmarking and analysis.

alevin-paper-pipeline

A crate to convert "complex" sequence library geometries to "simple" geometries

seq_geom_xform

Specification for the extended fragment geometry description language

efgdl-spec

seqproc

Testing out rust parsing of single-cell library geometry specifications

seq_geom_parser

roe

roers

A GitHub clone of the XZ repo (http://git.tukaani.org/xz.git) — not from the original author

protocol-estuary

Jsonnet

LabRules

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).

An attempt at rustification of the CQF (https://github.com/splatlab/cqf)

cqf-rust

libgff

splitp

split-seq preprocessing

quant-tx-diversity

alevin-fry-paper-scripts

scrna-ambiguity

This is a support website for Alevin-tool (part of Salmon).

alevin-tutorial

radicl-cpp

Internal library for basic reading and writing of .rad files in C++14

Get the "signature" of fasta files

FastaDigest

Reference Signatures (rs) in Rust (rs)

rsrs

libradicl

Documenting the (binary) output format used by Kallisto

simplr

KallistoFormatDescription

pufferfish_experiments

CSE549-txpCoverage

QuantAnalysis

Various tools for working with RAD files

radtk

A replicable and modular benchmark for long-read RNA transcript quantification methods

lr_quant_benchmarks