Aaron Lun's repositories
PseudoCount2018
Some thoughts on choosing an appropriate pseudo-count for log-transformation of scRNA-seq counts.
MoeDCPLogo
Making the DCP logo moe-r.
HVGDetection2018
Justification for the variance modelling and HVG detection methods in scran.
IndependentFilter2015
Some work detailing the independence of the NB mean as a filter statistic.
LazyAssayVectors
Lazily materialized assay vectors based on ALTREP.
ChIPSeqThoughts
Assorted thoughts on ChIP-seq practices and software, see https://ltla.github.io/ChIPSeqThoughts for the compiled version.
TravelsAroundTheWorld
Aaron's tips, tricks and general reminders for travelling around the world. Or at least to civilized places with internet connectivity.
BiocWorkCache
Testing the feasibility of knitr caching for Bioconductor workflows
chipseqDBResults
Compiled reference results for the chipseqDB workflow at https://github.com/LTLA/chipseqDB.
fugi
Further utilities for GenomicInteractions
FurtherMNN2018
Code for further development of the mutual nearest neighbours batch correction method, as implemented in the scran package.
GenomicInteractions
Clone of the Bioconductor repository for the GenomicInteractions package.
IndexedRelations
Bioconductor class to represent indexed relationships between features
Matrix
Fork of https://r-forge.r-project.org/scm/?group_id=61
plyexperiment
A fluent interface to SummarizedExperiment
rcpphnsw
Rcpp bindings for the approximate nearest neighbors library HNSW
RepertoireUtils
Utilities for analyzing repertoire sequencing data, to be used in the OSCA book.
simpleSingleCellResults
Compiled reference results for the simpleSingleCell workflow at https://github.com/MarioniLab/simpleSingleCell.
son.of.basilisk
Test package for the SPB to see if basilisk works.
tximport
Import and summarize transcript-level estimates for gene-level analysis