Pinned Repositories
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.
cuttlefish
Building the compacted de Bruijn graph efficiently from references or reads.
kmers
A bit-packed k-mer representation (and relevant utilities) for rust
oarfish
long read RNA-seq quantification
pufferfish
An efficient index for the colored, compacted, de Bruijn graph
RapMap
Rapid sensitive and accurate read mapping via quasi-mapping
salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
simpleaf
A rust framework to make using alevin-fry even simpler
terminus
wasabi
Prepare Sailfish and Salmon output for downstream analysis
COMBINE lab's Repositories
COMBINE-lab/RapClust
Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
COMBINE-lab/shoal
Improved multi-sample transcript abundance estimates using adaptive priors
COMBINE-lab/rainbowfish
A succinct colored dBG representation
COMBINE-lab/SkipPatch
dynamic-updateable-index
COMBINE-lab/GRASS
Graph-Regularized Annotation via Semi-Supervised learning
COMBINE-lab/continuous_analysis_rnaseq
Example of how continuous analysis can be used for RNA-Seq differential expression.
COMBINE-lab/matryoshka
Methods for the automated discovery of hierarchically-structured chromatin domains
COMBINE-lab/LabRules
A list of rules and hints (on various different subjects) for members of the COMBINE lab. Others may also find them useful.
COMBINE-lab/txome-clustering
Meaningful and efficient clustering of de novo transcriptome assembly results (better name pending).
COMBINE-lab/xz
A GitHub clone of the XZ repo (http://git.tukaani.org/xz.git) — not from the original author
COMBINE-lab/cqf-rust
An attempt at rustification of the CQF (https://github.com/splatlab/cqf)
COMBINE-lab/spdlog
Super fast C++ logging library.
COMBINE-lab/continuous_analysis
Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.
COMBINE-lab/CSE549-txpCoverage
COMBINE-lab/FastaDigest
Get the "signature" of fasta files
COMBINE-lab/jemalloc
COMBINE-lab/KallistoFormatDescription
Documenting the (binary) output format used by Kallisto
COMBINE-lab/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
COMBINE-lab/pufferfish_experiments
COMBINE-lab/QuantAnalysis
COMBINE-lab/selective-alignment-experiment
COMBINE-lab/BitSeqVB_benchmarking
BitSeqVB paper benchmarking experiments
COMBINE-lab/bwa
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
COMBINE-lab/combinelib
Assortment of random, potentially-useful utility functions and classes.
COMBINE-lab/cosmo
Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.
COMBINE-lab/easyhdf5
COMBINE-lab/polyester_simulation
Polyester simulation
COMBINE-lab/SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
COMBINE-lab/staden-io_lib
GitHub clone of SVN repo svn://svn.code.sf.net/p/staden/code/io_lib (cloned by http://svn2github.com/)
COMBINE-lab/Sux
Implementing Succinct Data Structures from Sebastiano Vigna(http://sux.di.unimi.it)