masoodzaka Goto Github PK

2019

acnviewer

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

ah_biopharma

BioPharma projects

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

awesome-awesomeness

A curated list of awesome awesomeness

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-bioinformatics-tools

A curated list of awesome Bioinformatics software, tools and resources

awesome-nextflow

A curated list of nextflow based pipelines

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bin

General-purpose repository for bioinformatics scripts

bio_tools

Useful bioinformatic scripts

bioinformatics-ca.github.io

repository for student workshop pages

bioinformatics-genome-assembly-and-analysis-workshop-pac-bio-and-10x-genomics-

Bioinformatics: Genome Assembly and Analysis Workshop [ Pac Bio and 10x Genomics ] - Dec 2016

bioinformatics-software

Bioinformatics software list

bioinformatics_docker_app

This docker app is collection of some of the most popular software currently being used in the analysis of next generation sequencing data.

circos

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

clustersploter

visualize genome features cluster(gene or other) and add synteny or crosslink among features or short/long reads mapping or snpindel or structural variants in vcf

cnaclinic

cnvscope

CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes

coloncancerwgbs

Six paired tumor-normal WGBS samples from Ziller et al. (2013) PMID: 23925113. Only chr22.

complexheatmap

Make Complex Heatmaps

copycat

a parallel R package for detecting copy-number alterations from short sequencing reads

copynumberanalysis

create-pptc-pdx-oncoprints

As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.

cruk-autumn-school-2017

CRUK Bioinformatics Workshop September 2017

cruk_ci_rnaseq_course

Base CRUK Cambridge Institute RNAseq Course

csbb-v3.0

CSBB - Computational Suite For Bioinformaticians and Biologists

dataset_tcga_firebrowse

Reference dataset for TCGA data pulled from firebrowse

deeplearning-biology

A list of deep learning implementations in biology