Pinned Repositories
annotatr
Annotation of Genomic Regions to Genomic Annotations
DDCV
A Visualized Shiny App to Evaluate Drug-Drug Interaction
EAGLE_LUAD
Genetic and Epigenetic Intratumor Heterogeneity Impacts Prognosis of Lung Adenocarcinoma
mSigPortal
Integrative mutational signature portal (MsigPortal) for cancer genomic study
Sherlock-Lung
Bioinformatic analysis scripts for Sherlock-Lung project
SigProfilerMatrixGenerator
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
SigProfilerPlotting
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
SigProfilerPlottingR
An R wrapper for running the SigProfilerPlotting framework
xtmgah's Repositories
xtmgah/Sherlock-Lung
Bioinformatic analysis scripts for Sherlock-Lung project
xtmgah/SigProfilerPlotting
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
xtmgah/Sherlock-Genome
Sherlock-Genome – A R Shiny App for Genomic Analysis and Visualization
xtmgah/CONIPHER-wrapper
xtmgah/CoRAL
Complete Reconstruction of Amplifications with Long reads
xtmgah/CSV-Filter
xtmgah/cue
Deep learning framework for SV calling and genotyping
xtmgah/deepsomatic
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
xtmgah/donutsk
Creating donut charts without a hassle
xtmgah/foldmason
Multiple Protein Structure Alignment at Scale with FoldMason
xtmgah/FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
xtmgah/gencube
xtmgah/GenomeMosaicMaker
Tool for copying read-alignments regions centered around variants (in VCF/VCF.GZ/BCF format) from existing genomes (in SAM/BAM/CRAM format) to insert them into canvas genomes (in SAM/BAM/CRAM format).
xtmgah/GenomeVariator
Tool for adding genomic variants to an existing genome (in SAM/BAM/CRAM format). Currently supported variants are SNVs, indels and SVs (insertions, deletions, translocations, inversions and duplications). It generates realistic genomes as almost always less than 99% of the original real genome is modified.
xtmgah/ggsankeyfier
Add alluvial / sankey diagram layers to a ggplot
xtmgah/gritic
A tool for timing complex copy number gains in cancer.
xtmgah/irescue
Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq
xtmgah/leviosam2
Fast and accurate coordinate conversion between assemblies
xtmgah/LongReadSum
xtmgah/LotOfCells
R package for analysing meaningful differences in the numbers of cell populations from single-cell phenotypic data
xtmgah/m6anet
Detection of m6A from direct RNA-Seq data
xtmgah/mhc-hammer
Pipeline to detect HLA disruption from WES and RNAseq data
xtmgah/minda
xtmgah/Monopogen
SNV calling from single cell sequencing
xtmgah/NIHCloudLabGCP
Documentation and tutorials on using GCP for biomedical research
xtmgah/plotsr
Tool to plot synteny and structural rearrangements between genomes
xtmgah/pyjacker
xtmgah/REViewer
A tool for visualizing alignments of reads in regions containing tandem repeats
xtmgah/scDRS
Single-cell disease relevance score (scDRS)
xtmgah/somrit
Somatic Retrotransposon Insertion Toolkit