Masood Zaka's repositories
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.
AH_BioPharma
BioPharma projects
alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome-bioinformatics-tools
A curated list of awesome Bioinformatics software, tools and resources
bio_tools
Useful bioinformatic scripts
CNVScope
CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
ComplexHeatmap
Make Complex Heatmaps
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.
deeplearning-biology
A list of deep learning implementations in biology
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
EvoFreq
Evolutionary frequency visualization tool of temporal data
FirebrowseR
An R client for broads firehose pipeline, providing TCGA data sets
gatk
Official code repository for GATK versions 4 and up
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
hmftools
Various utility tools for working with genomics data
infercnv
Inferring CNV from Single-Cell RNA-Seq
lab_scripts
Consolidated scripts used by the Morin lab
microbial_bioinformatics
Collection of the some of the most famous microbial genome data analysis tools.
mlr
mlr: Machine Learning in R
PySyft
A library for encrypted, privacy preserving machine learning
python-data-science
Python3 teaching materials for data science (2 days)
rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
Snakemake_smallRNASeq
Small RNA-seq analysis using bowtie, featureCounts and Salmon tools.
vcfR
Tools to work with variant call format files