COMBINE lab (@COMBINE-lab)
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COMBINE-lab

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Top repositories

1

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
C++
765
star
2

alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Rust
159
star
3

pufferfish

An efficient index for the colored, compacted, de Bruijn graph
C
107
star
4

RapMap

Rapid sensitive and accurate read mapping via quasi-mapping
C++
89
star
5

cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.
C++
77
star
6

oarfish

long read RNA-seq quantification
Rust
66
star
7

terminus

Rust
57
star
8

kmers

A bit-packed k-mer representation (and relevant utilities) for rust
Rust
47
star
9

simpleaf

A rust framework to make using alevin-fry even simpler
Rust
44
star
10

wasabi

Prepare Sailfish and Salmon output for downstream analysis
R
43
star
11

SalmonTools

Useful tools for working with Salmon output
C++
36
star
12

RapClust

Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
Python
30
star
13

piscem

Rust wrapper for the next generation (still currently in C++)
Rust
20
star
14

shoal

Improved multi-sample transcript abundance estimates using adaptive priors
C++
20
star
15

grangers

Rust
16
star
16

pufferfish2

Rust
15
star
17

EDS

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format
Rust
15
star
18

pyroe

Python
15
star
19

grouper

Python
15
star
20

piscem-infer

Rust
14
star
21

mazu

A Rust library for building modular, fast and compact indexes over genomic data
Rust
13
star
22

rainbowfish

A succinct colored dBG representation
C++
12
star
23

quark

semi-reference-based short read compression
C++
11
star
24

minnow

C++
10
star
25

usefulaf

Useful scripts and tools related to alevin-fry
Rust
9
star
26

measuresmatter

A treatise on quantification and differential expression from RNA-seq data
8
star
27

combine-lab.github.io

HTML
8
star
28

quantaf

Nextflow
8
star
29

seine-rs

A (rust)🦀 library and suite of tools for manipulating and processing the output of salmon, alevin, and alevin-fry 🐟
Rust
7
star
30

piscem-cpp

A small sparse and fast reference index based on SShash and Tiling encoding
C
6
star
31

sc-census

R
6
star
32

GRASS

Graph-Regularized Annotation via Semi-Supervised learning
Python
6
star
33

TreeTerminus

C
5
star
34

COMBINE-lab.github.io-OLD

Lab website
HTML
5
star
35

matryoshka

Methods for the automated discovery of hierarchically-structured chromatin domains
C++
5
star
36

forseti

Python
5
star
37

pcalib

A small "lightweight" implementation of PCA in C++ using the Eigen library
C++
5
star
38

perplexity

Rust
5
star
39

alevin-paper-pipeline

A simple pipeline using CGAT framework for benchmarking and analysis.
Python
5
star
40

seq_geom_xform

A crate to convert "complex" sequence library geometries to "simple" geometries
Rust
4
star
41

efgdl-spec

Specification for the extended fragment geometry description language
4
star
42

seqproc

Rust
4
star
43

seq_geom_parser

Testing out rust parsing of single-cell library geometry specifications
Rust
4
star
44

roe

R
3
star
45

roers

Rust
3
star
46

protocol-estuary

Jsonnet
3
star
47

xz

A GitHub clone of the XZ repo (http://git.tukaani.org/xz.git) — not from the original author
C
3
star
48

LabRules

A list of rules and hints (on various different subjects) for members of the COMBINE lab. Others may also find them useful.
3
star
49

txome-clustering

Meaningful and efficient clustering of de novo transcriptome assembly results (better name pending).
Python
3
star
50

cqf-rust

An attempt at rustification of the CQF (https://github.com/splatlab/cqf)
C
2
star
51

libgff

C++
2
star
52

splitp

split-seq preprocessing
Rust
2
star
53

quant-tx-diversity

Jupyter Notebook
2
star
54

alevin-fry-paper-scripts

Jupyter Notebook
2
star
55

scrna-ambiguity

Jupyter Notebook
2
star
56

alevin-tutorial

This is a support website for Alevin-tool (part of Salmon).
1
star
57

radicl-cpp

Internal library for basic reading and writing of .rad files in C++14
C++
1
star
58

FastaDigest

Get the "signature" of fasta files
Python
1
star
59

rsrs

Reference Signatures (rs) in Rust (rs)
Rust
1
star
60

libradicl

Rust
1
star
61

simplr

1
star
62

KallistoFormatDescription

Documenting the (binary) output format used by Kallisto
1
star
63

pufferfish_experiments

Jupyter Notebook
1
star
64

CSE549-txpCoverage

C++
1
star
65

QuantAnalysis

Jupyter Notebook
1
star
66

radtk

Various tools for working with RAD files
Rust
1
star
67

lr_quant_benchmarks

A replicable and modular benchmark for long-read RNA transcript quantification methods
Python
1
star