Discover COMBINE-lab/alevin-fry-paper-scripts 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

Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes

RapClust

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

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