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Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
A 3D barplot script for R. Can encode variables using both height and depth of columns.
Software to compute reproducibility and quality scores for Hi-C data
WebGL accelerated JavaScript molecular graphics library
my github public profile
Allele-specific Binding from Chip-seq
ACE: Accurate Correction of Errors
Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
ActiveDriverWGSR is an R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data
Ad-ins and keyboard shortcuts for building calculation pipelines in R
ADmiRE: Annotative Database of miRNA Elements
Advanced R programming: a book
Calculates allelic Fold Change (aFC) using standard input files for fastQTL.
Python package to annotate and visualize gene fusions.
Web app for AGFusion
a rapid and flexible tool for aggregation plots
AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at http://arxiv.org/abs/1912.08735)
Support code for NGS copy number algorithms
Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.
Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GrCH37 reference sequence and one or more regions of interest. This is development version. Please "watch" this repository for production release and methods manuscript soon.
R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al. (https://doi.org/10.1038/s41467-020-14286-0)
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
R data package for annotating/converting Gene IDs
Annotation of Genomic Regions to Genomic Annotations
Hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.