xtmgah Goto Github PK

2020plus

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

3dbarplot

A 3D barplot script for R. Can encode variables using both height and depth of columns.

3dchromatin_replicateqc

Software to compute reproducibility and quality scores for Hi-C data

3dmol.js

WebGL accelerated JavaScript molecular graphics library

5pl1sc

aaronmck.github.io

my github public profile

abc

Allele-specific Binding from Chip-seq

acat

ace

ACE: Accurate Correction of Errors

acnviewer

Comprehensive genome-wide visualization of absolute copy number and copy neutral variations

activedriverwgsr

ActiveDriverWGSR is an R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data

addinexampleswv

Ad-ins and keyboard shortcuts for building calculation pipelines in R

admire

ADmiRE: Annotative Database of miRNA Elements

adv-r

Advanced R programming: a book

afc

Calculates allelic Fold Change (aFC) using standard input files for fastQTL.

agfusion

Python package to annotate and visualize gene fusions.

agfusionweb

Web app for AGFusion

agplus

a rapid and flexible tool for aggregation plots

airlift

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)

allelecount

Support code for NGS copy number algorithms

allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

allelicimbalance

alleloscope

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

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.

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

annotables

R data package for annotating/converting Gene IDs

annotatr

Annotation of Genomic Regions to Genomic Annotations

apobec3b

apolloh

Hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020