Pinned Repositories
asap_to_kite
CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing
Bio-Tools-Primer3Redux
A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2
biopython
Official git repository for Biopython (converted from CVS)
chromVAR
chromatin Variability Across Regions (of the genome!)
CopywriteR
DNA copy number detection from off-target sequence data
DataVis
Using a bubble chart to demonstrate that from a dataset of 1,157 baseball players, right-handed players have lower batteling average and home run counts.
dendextend
Extending R's Dendrogram Functionality
JohnMCMa's Repositories
JohnMCMa/Bio-Tools-Primer3Redux
A reimplementation of BioPerl's Primer3-related code for primer3 v1 and v2
JohnMCMa/asap_to_kite
CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing
JohnMCMa/biopython
Official git repository for Biopython (converted from CVS)
JohnMCMa/chromVAR
chromatin Variability Across Regions (of the genome!)
JohnMCMa/CopywriteR
DNA copy number detection from off-target sequence data
JohnMCMa/DataVis
Using a bubble chart to demonstrate that from a dataset of 1,157 baseball players, right-handed players have lower batteling average and home run counts.
JohnMCMa/dendextend
Extending R's Dendrogram Functionality
JohnMCMa/ensembl-vep
The Variant Effect Predictor predicts the functional effects of genomic variants
JohnMCMa/epic2
Ultraperformant reimplementation of SICER
JohnMCMa/histoneHMM
Differential peak calling tool for ChIP-seq data
JohnMCMa/HLAminer
HLA predictions from NGS shotgun data
JohnMCMa/hotspot3d
3D hotspot mutation proximity analysis tool
JohnMCMa/intermine
A powerful open source data warehouse system
JohnMCMa/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
JohnMCMa/MuPeXI
MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
JohnMCMa/nucleus
Python and C++ code for reading and writing genomics data.
JohnMCMa/OptiType
Precision HLA typing from next-generation sequencing data
JohnMCMa/parliament2
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
JohnMCMa/phaser
phasing and Allele Specific Expression from RNA-seq
JohnMCMa/pindel
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
JohnMCMa/sc_read_kallisto_wrapper
wrapper for single cell transcriptomics pipeline with kallisto
JohnMCMa/SCITO-seq
SCITO-seq related, forked from original code
JohnMCMa/seurat
R toolkit for single cell genomics
JohnMCMa/tracer
TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
JohnMCMa/ud120
JohnMCMa/vcf_parser
Simple vcf parser, based on PyVCF
JohnMCMa/vcftools
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
JohnMCMa/VEP_plugins
Plugins for the Ensembl Variant Effect Predictor (VEP)
JohnMCMa/XenofilteR
Filtering of PDX samples for mouse derived reads