LTLA/gesel.js

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MIT License
Created over 1 year ago
Updated 12 months ago

LTLA/gesel.js

LTLA

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Client-side gene set queries.

SingleR

Clone of the Bioconductor repository for the SingleR package.

SingleCellThoughts

Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.

umappp

UMAP C++ implementation

celldex

Collection of cell type reference datasets.

scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.

batchelor

Clone of the Bioconductor repository for the batchelor package.

knncolle

Collection of KNN algorithms in C++

scran.chan

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

CppIrlba

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

TileDBArray

Clone of the Bioconductor repository for the TileDBArray package.

SingleRBook-base

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

PseudoCount2018

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

archive-beachmat

An archived version of the beachmat repository, see https://github.com/LTLA/beachmat for the active version.

Counterspell2018

UU: Counter target spell.

CppWeightedLowess

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

MoeDCPLogo

Making the DCP logo moe-r.

libscran

scran, but in C++.

scuttle

Clone of the Bioconductor repository for the scuttle package.

qdtsne

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

HumanCellAtlasData

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

rds2cpp

Read and write RDS files in C++

HVGDetection2018

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

BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.

BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.

ParquetDataFrame

Bioconductor-friendly bindings for Parquet files.

CppKmeans

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

artsc

Single-cell-related art, which may or may not be scientifically useful. But hey, it's pretty.

SingleRBook

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

tatami

C++ API for various matrix types.

bakana

Backend compute for kana

archive-csaw

An archived version of the csaw repository, see https://github.com/LTLA/csaw for the active version.

uzuki

Safely saving R lists to JSON

CppMnnCorrect

A C++ implementation of the MNN correction algorithm

yaumap

Yet Another UMAP package for R

PCSelection2018

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

csawUsersGuide

Clone of the Bioconductor repository for the csawUsersGuide workflow.

MatrixEval2017

Evaluating access and memory usage of different matrix types

SummarizedExperiments.jl

Julia implementation of Bioconductor's SummarizedExperiment class

rebook

Clone of the Bioconductor repository for the rebook package.

beachmat

Clone of the Bioconductor repository for the beachmat package.

scran-cli

A command line interface to scran

MultiAssayExperiments.jl

Julia implementation of Bioconductor's MultiAssayExperiment.

gesel-feedstock

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

diffHic

Clone of the Bioconductor repository for the diffHic package.

LazyAssayVectors

Lazily materialized assay vectors based on ALTREP.

bluster

Clone of the Bioconductor repository for the bluster package.

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

TrojanBookBuilder

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

wasmarrays.js

Memory-management wrapper around arrays on the Wasm heap.

byteme

C++ utilities for simple buffered inputs.

csaw

Clone of the Bioconductor repository for the csaw package.

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++

metapod

Clone of the Bioconductor repository for the metapod package.

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.

igraph-wasm

Compiled Wasm binaries for the igraph C library

crio

CellRanger input/output

kana-feature-sets

Prebuilt feature sets for use in kana's GSEA

bioconductor.js

Javascript implementations of common Bioconductor classes

DebuggingSpectra

Various files for debugging the Spectra library.

chipseqDB

Clone of the Bioconductor repository for the chipseqDB workflow.

kaori

C++ library for barcode counting

CRUKtools

Assorted scripts for running server jobs at CRUK CI

raticate

R bindings for tatami matrices

gesel-app

A demonstration UI for the gesel library.

main2master

Convert your main branch back to its rightful name.

actions-anime-gif-slackbot

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

gesel-manuscript

Manuscript for the gesel NPM package.

anime-slack-cronjob

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

uzuki2

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

scran.jl

Julia bindings for the libscran library.

aggregate-demonstrator

Demonstration of how to vendor aggregateAcrossCells

TravelsAroundTheWorld

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

BumpyMatrix

Clone of the Bioconductor repository for the BumpyMatrix package.

OddsAndEnds

Miscellaneous code fragments that don't belong anywhere else.

csawBook

The book of the package.

singlepp

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

ResidualMatrix

Clone of the Bioconductor repository for the ResidualMatrix package.

ChIPSeqThoughts

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

GenomicFeatureVectors.jl

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

acceptable-anime-gifs-api

REST API for serving anime GIFs on a Cloudflare Worker