lianos
Closing the gap between computational- and bench- scientists // #rstats oR bust!
San Francisco, CA
Pinned Repositories
FacileAnalysis
Modular & interactive analysis components for bioinformatics
FacileData
A fluent, tidy-like API for accessing multi-assay high-throughput genomics data
buckshot
An R interface to "shotgun", a parallel lasso and sparse logistic regression solver written in C++
fastx-toolkit
C Library to work with fasta/q files
multiGSEA
NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
papers-bin
Run commands against your Papers2 database from the command line
seqtools
Utilities to deal with sequencing data
shikken
A more R-idiomatic wrapper to the shogun toolbox.
sparrow
Take command of your set enrichment analyses.
sparrow.shiny
Provides shiny components to visualize sparrow GSEA results
lianos's Repositories
lianos/multiGSEA
NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
lianos/sparrow
Take command of your set enrichment analyses.
lianos/papers-bin
Run commands against your Papers2 database from the command line
lianos/seqtools
Utilities to deal with sequencing data
lianos/buckshot
An R interface to "shotgun", a parallel lasso and sparse logistic regression solver written in C++
lianos/fastx-toolkit
C Library to work with fasta/q files
lianos/shikken
A more R-idiomatic wrapper to the shogun toolbox.
lianos/biosignals
Smooth, find peaks and edges in 1D signal vectors.
lianos/multiGSEA.shiny
Provides shiny components to visualize multilGSEA results
lianos/Rx
Eases some of the pain when using Sublime Text 2 to code in R
lianos/ARE.utils
A conglomeration of utilities that aren't project specific and use in my R day-to-day
lianos/BiocSeqSVM
Pedagogical machine learning exercises for NGS data
lianos/moin-mule
Utility that enables sending file attachments to MoinMoin wikis from the command line
lianos/GenomicCache
Extensions to Bioconductor GenomicFeatures package. Primarily, this implements a more "Gene Centric" view on the world, as opposed to base GenomicFeature's transcript/exon/cds centric view.
lianos/my-emacs
A clean slate for my .emacs.d confs
lianos/sparrow.shiny
Provides shiny components to visualize sparrow GSEA results
lianos/dotfiles
A repository to store useful ~/.dotfiles
lianos/DT
R Interface to the jQuery Plug-in DataTables
lianos/fishpond
Fishpond: differential transcript and gene expression with inferential replicates
lianos/GeneSetDb.MSigDB.Hsapiens.v61
Deprecated by GeneSetDb.MSigDB. This repository is only to be used with multiGSEA@prebioc.
lianos/GeneSetDb.MSigDB.Mmusculus.v61
Deprecated by GeneSetDb.MSigDB. This repository is only to be used with multiGSEA@prebioc.
lianos/GvizX
Extensions to Gviz
lianos/lianos.github.io
Personal web presence using blogdown + netlify
lianos/msigdb.data
Provides versioned MSigDB collections with ability to ortholog map to other species.
lianos/msigdbr
MSigDB gene sets for multiple organisms in a tidy data format
lianos/SeqGL
SeqGL is a group lasso based algorithm to extract TF sequence signals from ChIP, DNase and ATAC-seq profiles
lianos/TagSeq-original
Analysis of tag based high-throughput sequencing protocols
lianos/universe
Configuration for https://lianos.r-universe.dev/