vd4mmind

GEN242

Class: Data Analysis in Genome Biology

qupath

QuPath - Open Source Digital Pathology

RNASeq

This project consists of various scripts that were used for analysis of RNA-Seq data. The scripts are not customised but basal level which one can use to fit into their suitable experimental design post modifications.

RStats_Biology

I will put R and Statistics Tutorials in this one for future resources in the field of Biology

MOFA

Multi-Omics Factor Analysis

ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

MICMIC

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

atac-seq-pipeline

ENCODE ATAC-seq pipeline

ClinicalGradeDNAseq

Automated next generation DNA sequencing analysis pipeline suited for clinical tests, with >99.9% sensitivity to Sanger sequencing at read-depth>18

quack

Machine learning algorithm to predict biological pathway relationships based on functional genomics networks

MOFA_analysis

Scripts to analyse CLL data in MOFA paper

Rcade

Games to procrastinate with RStudio

SnpEff

ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ASCEND)

deeplift

Public facing deeplift repo

SnpSift

datasharing

The Leek group guide to data sharing

EnhancedVolcano

Volcano plot with enhanced colouring and labeling

Deep-Neural-Networks-HealthCare

Tangible and Practical Deep Learning Projects Repository for Healthcare such as Cancer, Drug Discovery, Genomic and More

DMSO

git-guide

ngs-filters

Filters for false-positive mutation calls in NGS

scRNA.seq.course

Analysis of single cell RNA-seq data course, Cambridge University, UK

GOexpress

Analysies of gene expression data using Gene Ontology

awesome-single-cell

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

bioStars.ref

Some hacks that are pretty useful in day to day activities for Bioinformatics , handy as cheatsheets

sevenbridges-r

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets