Discover LTLA/batchelor Open Source project by Aaron Lun (@LTLA)

umappp

UMAP C++ implementation

Collection of cell type reference datasets.

celldex

scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.

knncolle

Collection of KNN algorithms in C++

A slimmed down version of scran, based on the C++ library of the same name.

scran.chan

CppIrlba

A C++ port of the IRLBA algorithm, based on the C code in the R package.

Clone of the Bioconductor repository for the TileDBArray package.

TileDBArray

SingleRBook-base

See https://github.com/LTLA/SingleRBook for the latest version of this content.

Some thoughts on choosing an appropriate pseudo-count for log-transformation of scRNA-seq counts.

PseudoCount2018

An archived version of the beachmat repository, see https://github.com/LTLA/beachmat for the active version.

archive-beachmat

UU: Counter target spell.

Counterspell2018

A standalone C++ implementation of limma::weightedLowess.

CppWeightedLowess

Making the DCP logo moe-r.

MoeDCPLogo

libscran

scran, but in C++.

Clone of the Bioconductor repository for the scuttle package.

scuttle

qdtsne

A quick-and-dirty t-SNE implementation as a header-only library

R/Bioconductor-based access to single-cell genomics data generated by the Human Cell Atlas Project.

HumanCellAtlasData

rds2cpp

Read and write RDS files in C++

Justification for the variance modelling and HVG detection methods in scran.

HVGDetection2018

Clone of the Bioconductor repository for the BiocSingular package.

BiocSingular

BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.

Bioconductor-friendly bindings for Parquet files.

ParquetDataFrame

CppKmeans

C++ port of R's Hartigan-Wong implementation

The package wrapping the book, for deployment via the Bioconductor build system.

artsc

SingleRBook

C++ API for various matrix types.

tatami

bakana

Backend compute for kana

Client-side gene set queries.

gesel.js

An archived version of the csaw repository, see https://github.com/LTLA/csaw for the active version.

archive-csaw

uzuki

Safely saving R lists to JSON

A C++ implementation of the MNN correction algorithm

CppMnnCorrect

Yet Another UMAP package for R

yaumap

Some comments on how to determine the number of PCs to retain.

PCSelection2018

Clone of the Bioconductor repository for the csawUsersGuide workflow.

csawUsersGuide

MatrixEval2017

Evaluating access and memory usage of different matrix types

Julia implementation of Bioconductor's SummarizedExperiment class

SummarizedExperiments.jl

Clone of the Bioconductor repository for the rebook package.

rebook

beachmat

Clone of the Bioconductor repository for the beachmat package.

A command line interface to scran

scran-cli

Julia implementation of Bioconductor's MultiAssayExperiment.

MultiAssayExperiments.jl

Generate pre-built gesel indices for client-side gene set search.

gesel-feedstock

diffHic

Clone of the Bioconductor repository for the diffHic package.

LazyAssayVectors

Lazily materialized assay vectors based on ALTREP.

Clone of the Bioconductor repository for the bluster package.

bluster

tsvd

Truncated SVD algorithms in C++

IndependentFilter2015

Some work detailing the independence of the NB mean as a filter statistic.

DropletTestFiles

Clone of the Bioconductor repository for the DropletTestFiles package.

subpar

Substitutable parallelization for C++ libraries

Sneak books onto the Bioconductor build system with a trojan package.

TrojanBookBuilder

wasmarrays.js

Memory-management wrapper around arrays on the Wasm heap.

C++ utilities for simple buffered inputs.

byteme

Clone of the Bioconductor repository for the csaw package.

csaw

acceptable-anime-gifs

A curated set of GIFs that are reasonably SFW, primarily used to power annoying Slackbots.

aarand

Aaron's random distributions for C++

Clone of the Bioconductor repository for the metapod package.

metapod

archive-InteractionSet

An archived version of the InteractionSet repository, see https://github.com/LTLA/InteractionSet for the active version.

InteractionSet

Clone of the Bioconductor repository for the InteractionSet package, see https://bioconductor.org/packages/devel/bioc/html/InteractionSet.html for the official development version.

HDF5Arrays.jl

Julia implementation of Bioconductor's HDF5Array class.

Compiled Wasm binaries for the igraph C library

igraph-wasm

CMake

crio

CellRanger input/output

kana-feature-sets

Prebuilt feature sets for use in kana's GSEA

bioconductor.js

Javascript implementations of common Bioconductor classes

Various files for debugging the Spectra library.

DebuggingSpectra

Clone of the Bioconductor repository for the chipseqDB workflow.

chipseqDB

kaori

C++ library for barcode counting

Assorted scripts for running server jobs at CRUK CI

CRUKtools

Shell

raticate

R bindings for tatami matrices

A demonstration UI for the gesel library.

gesel-app

Convert your main branch back to its rightful name.

main2master

Shell

actions-anime-gif-slackbot

Post anime GIFs to Slack as a GitHub Action. What better way to annoy your co-workers?

Python

gesel-manuscript

Manuscript for the gesel NPM package.

Hosts GitHub Actions that posts anime GIFs to my various slack channels.

anime-slack-cronjob

uzuki2

R lists to HDF5... or JSON, I suppose

Julia bindings for the libscran library.

scran.jl

Demonstration of how to vendor aggregateAcrossCells

aggregate-demonstrator

Aaron's tips, tricks and general reminders for travelling around the world. Or at least to civilized places with internet connectivity.

TravelsAroundTheWorld

BumpyMatrix

Clone of the Bioconductor repository for the BumpyMatrix package.

OddsAndEnds

Miscellaneous code fragments that don't belong anywhere else.

Shell

csawBook

The book of the package.

Pure C++ implementation of the SingleR method for cell type annotation

singlepp

Clone of the Bioconductor repository for the ResidualMatrix package.

ResidualMatrix

ChIPSeqThoughts

Assorted thoughts on ChIP-seq practices and software, see https://ltla.github.io/ChIPSeqThoughts for the compiled version.

Makefile

GenomicFeatureVectors.jl

Julia implementation of Bioconductor's GenomicRanges(List) infrastructure.

REST API for serving anime GIFs on a Cloudflare Worker

acceptable-anime-gifs-api