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  • Created over 6 years ago
  • Updated about 5 years ago

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Repository Details

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

More Repositories

1

SingleR

Clone of the Bioconductor repository for the SingleR package.
R
158
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2

SingleCellThoughts

Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.
TeX
41
star
3

umappp

UMAP C++ implementation
C++
38
star
4

celldex

Collection of cell type reference datasets.
R
35
star
5

scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.
R
21
star
6

batchelor

Clone of the Bioconductor repository for the batchelor package.
R
16
star
7

knncolle

Collection of KNN algorithms in C++
C++
11
star
8

scran.chan

A slimmed down version of scran, based on the C++ library of the same name.
R
10
star
9

CppIrlba

A C++ port of the IRLBA algorithm, based on the C code in the R package.
C++
10
star
10

TileDBArray

Clone of the Bioconductor repository for the TileDBArray package.
R
10
star
11

SingleRBook-base

See https://github.com/LTLA/SingleRBook for the latest version of this content.
TeX
10
star
12

PseudoCount2018

Some thoughts on choosing an appropriate pseudo-count for log-transformation of scRNA-seq counts.
TeX
9
star
13

archive-beachmat

An archived version of the beachmat repository, see https://github.com/LTLA/beachmat for the active version.
C++
8
star
14

Counterspell2018

UU: Counter target spell.
TeX
8
star
15

CppWeightedLowess

A standalone C++ implementation of limma::weightedLowess.
C++
8
star
16

MoeDCPLogo

Making the DCP logo moe-r.
8
star
17

libscran

scran, but in C++.
C++
7
star
18

scuttle

Clone of the Bioconductor repository for the scuttle package.
R
7
star
19

qdtsne

A quick-and-dirty t-SNE implementation as a header-only library
C++
7
star
20

HumanCellAtlasData

R/Bioconductor-based access to single-cell genomics data generated by the Human Cell Atlas Project.
R
7
star
21

rds2cpp

Read and write RDS files in C++
C++
6
star
22

HVGDetection2018

Justification for the variance modelling and HVG detection methods in scran.
TeX
6
star
23

BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.
R
6
star
24

BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.
C++
6
star
25

ParquetDataFrame

Bioconductor-friendly bindings for Parquet files.
R
5
star
26

CppKmeans

C++ port of R's Hartigan-Wong implementation
C++
5
star
27

artsc

Single-cell-related art, which may or may not be scientifically useful. But hey, it's pretty.
R
5
star
28

SingleRBook

The package wrapping the book, for deployment via the Bioconductor build system.
TeX
5
star
29

tatami

C++ API for various matrix types.
C++
5
star
30

bakana

Backend compute for kana
JavaScript
5
star
31

gesel.js

Client-side gene set queries.
JavaScript
5
star
32

archive-csaw

An archived version of the csaw repository, see https://github.com/LTLA/csaw for the active version.
R
5
star
33

uzuki

Safely saving R lists to JSON
C++
4
star
34

CppMnnCorrect

A C++ implementation of the MNN correction algorithm
C++
4
star
35

yaumap

Yet Another UMAP package for R
C++
4
star
36

PCSelection2018

Some comments on how to determine the number of PCs to retain.
TeX
4
star
37

csawUsersGuide

Clone of the Bioconductor repository for the csawUsersGuide workflow.
4
star
38

MatrixEval2017

Evaluating access and memory usage of different matrix types
TeX
4
star
39

SummarizedExperiments.jl

Julia implementation of Bioconductor's SummarizedExperiment class
Julia
4
star
40

rebook

Clone of the Bioconductor repository for the rebook package.
R
4
star
41

beachmat

Clone of the Bioconductor repository for the beachmat package.
C++
3
star
42

scran-cli

A command line interface to scran
C++
3
star
43

MultiAssayExperiments.jl

Julia implementation of Bioconductor's MultiAssayExperiment.
Julia
3
star
44

gesel-feedstock

Generate pre-built gesel indices for client-side gene set search.
R
3
star
45

diffHic

Clone of the Bioconductor repository for the diffHic package.
R
3
star
46

LazyAssayVectors

Lazily materialized assay vectors based on ALTREP.
C++
2
star
47

bluster

Clone of the Bioconductor repository for the bluster package.
R
2
star
48

tsvd

Truncated SVD algorithms in C++
2
star
49

IndependentFilter2015

Some work detailing the independence of the NB mean as a filter statistic.
R
2
star
50

DropletTestFiles

Clone of the Bioconductor repository for the DropletTestFiles package.
R
2
star
51

subpar

Substitutable parallelization for C++ libraries
C++
2
star
52

TrojanBookBuilder

Sneak books onto the Bioconductor build system with a trojan package.
R
2
star
53

wasmarrays.js

Memory-management wrapper around arrays on the Wasm heap.
JavaScript
2
star
54

byteme

C++ utilities for simple buffered inputs.
C++
2
star
55

csaw

Clone of the Bioconductor repository for the csaw package.
R
2
star
56

acceptable-anime-gifs

A curated set of GIFs that are reasonably SFW, primarily used to power annoying Slackbots.
2
star
57

aarand

Aaron's random distributions for C++
C++
2
star
58

metapod

Clone of the Bioconductor repository for the metapod package.
R
2
star
59

archive-InteractionSet

An archived version of the InteractionSet repository, see https://github.com/LTLA/InteractionSet for the active version.
R
2
star
60

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.
R
2
star
61

HDF5Arrays.jl

Julia implementation of Bioconductor's HDF5Array class.
Julia
1
star
62

igraph-wasm

Compiled Wasm binaries for the igraph C library
CMake
1
star
63

crio

CellRanger input/output
R
1
star
64

kana-feature-sets

Prebuilt feature sets for use in kana's GSEA
R
1
star
65

bioconductor.js

Javascript implementations of common Bioconductor classes
JavaScript
1
star
66

DebuggingSpectra

Various files for debugging the Spectra library.
C++
1
star
67

chipseqDB

Clone of the Bioconductor repository for the chipseqDB workflow.
1
star
68

kaori

C++ library for barcode counting
C++
1
star
69

CRUKtools

Assorted scripts for running server jobs at CRUK CI
Shell
1
star
70

raticate

R bindings for tatami matrices
C++
1
star
71

gesel-app

A demonstration UI for the gesel library.
JavaScript
1
star
72

main2master

Convert your main branch back to its rightful name.
Shell
1
star
73

actions-anime-gif-slackbot

Post anime GIFs to Slack as a GitHub Action. What better way to annoy your co-workers?
Python
1
star
74

gesel-manuscript

Manuscript for the gesel NPM package.
TeX
1
star
75

anime-slack-cronjob

Hosts GitHub Actions that posts anime GIFs to my various slack channels.
1
star
76

uzuki2

R lists to HDF5... or JSON, I suppose
C++
1
star
77

scran.jl

Julia bindings for the libscran library.
Julia
1
star
78

aggregate-demonstrator

Demonstration of how to vendor aggregateAcrossCells
C++
1
star
79

BumpyMatrix

Clone of the Bioconductor repository for the BumpyMatrix package.
R
1
star
80

OddsAndEnds

Miscellaneous code fragments that don't belong anywhere else.
Shell
1
star
81

csawBook

The book of the package.
TeX
1
star
82

singlepp

Pure C++ implementation of the SingleR method for cell type annotation
C++
1
star
83

ResidualMatrix

Clone of the Bioconductor repository for the ResidualMatrix package.
R
1
star
84

ChIPSeqThoughts

Assorted thoughts on ChIP-seq practices and software, see https://ltla.github.io/ChIPSeqThoughts for the compiled version.
Makefile
1
star
85

GenomicFeatureVectors.jl

Julia implementation of Bioconductor's GenomicRanges(List) infrastructure.
Julia
1
star
86

acceptable-anime-gifs-api

REST API for serving anime GIFs on a Cloudflare Worker
JavaScript
1
star