M. Brown's repositories
VirusFinder2_VERSE
A copy of VirusFinder2/VERSE, used for identifying viral integrations.
nhlplusminus
An analysis of NHL player plus-minus using python
ctat-mutations
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
CTAT-SPLICING
detection of cancer splicing aberrations
fflr
Get ESPN fantasy football data in R
HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
infercnv
Inferring CNV from Single-Cell RNA-Seq
infercnvApp
This is an R shiny app created as a user friendly way to run the R package infercnv. Infercnv is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. More information on infercnv can be found on the infercnv Github Page
infercnvNGCHM
inferCNV interface to using NGCHM next generation heat maps
nf-VIF
A Nextflow-based Virus Insertion Finder
NGCHMR
An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)
nhlplusminusR
Basic NHL plus-minus analysis using R
RnaVariantBenchmarking
code for running alternative rna-based variant detection tools and benchmarking
RVBLR
This is a reimplementation of the RVBoost code.
SNPiR-Python
Python implementation of the original SNPiR code
ViFi
Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
ViralFusionSeq
Accurately discover viral integration events and fusion transcripts
VirTect
Detection of viruses from RNA-Seq on human samples
VIRUSBreakend
WDL for running PapenfussLab's VIRUSBreakend