Aaron Lun's repositories
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An archived version of the beachmat repository, see https://github.com/LTLA/beachmat for the active version.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.
HumanCellAtlasData
R/Bioconductor-based access to single-cell genomics data generated by the Human Cell Atlas Project.
archive-csaw
An archived version of the csaw repository, see https://github.com/LTLA/csaw for the active version.
MatrixEval2017
Evaluating access and memory usage of different matrix types
PCSelection2018
Some comments on how to determine the number of PCs to retain.
archive-InteractionSet
An archived version of the InteractionSet repository, see https://github.com/LTLA/InteractionSet for the active version.
IndependentFilter2015
Some work detailing the independence of the NB mean as a filter statistic.
ChIPSeqThoughts
Assorted thoughts on ChIP-seq practices and software, see https://ltla.github.io/ChIPSeqThoughts for the compiled version.
OddsAndEnds
Miscellaneous code fragments that don't belong anywhere else.
aaronlab
Aaron's workshop for Bioconductor 2015
archive-chipseqDB
An archived version of the chipseqDB repository, see https://github.com/LTLA/chipseqDB for the active version.
archive-diffHic
An archived version of the diffHic repository, see https://github.com/LTLA/diffHic for the active version.
BiocISet2016
Technical note for the InteractionSet package
BiocWorkCache
Testing the feasibility of knitr caching for Bioconductor workflows
FurtherNorm2018
Code for further development of the summation-based scaling normalization method, as implemented in the scran package.
giut
Improved genome-wide IUTs
OkNN2018
Code for performance testing of the kmknn package at https://github.com/LTLA/kmknn.
plyexperiment
A fluent interface to SummarizedExperiment
rcpphnsw
Rcpp bindings for the approximate nearest neighbors library HNSW
Rtsne
R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding
RtsneTestSuite
Tests the Rtsne package against the original bhtsne implementation.
RunTimeLinksViaR
Proof of concept for run-time linking of C++ libraries via R
sarlacc
The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, clusters reads and produces a consensus sequence for each cluster after multiple sequence alignment.
XenoSplit
Mapping pipeline