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genomemedicine_ngs_preliminaryprocessing

Lecture for Genome Medicine Bioinformatics Module on the file formats used in NGS data

genstats

Statistics course for JHU Genomic Data Science Sequence

ggpy

ggplot port for python

giotto

Single-cell spatial analysis toolbox

graphalignmentviewer

guessing_game

UNIX WORKBENCH Peer-graded Assignment

h3agwas

GWAS Pipeline for H3Africa

histomicstk

A Python library for pathology image analysis algorithms.

histoqc

HistoQC is an open-source quality control tool for digital pathology slides

hpcuk-website

Source for the HPC-UK website

icliplib

Tools for dealing with iCLIP data

idep-rstudio

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

imagej-intro

Analyzing fluorescence microscopy images with ImageJ

intro-rnaseq-jupyter

Building RNA-seq Analysis Pipelines with Jupyter

isoformswitchanalyzer

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)

jnb_reproducible

📓Notebook materials for the RSE conference workshop (2017)

jupyter-genomics

A collection of Jupyter notebooks authored by the UCSD Center for Computational Biology & Bioinformatics (http://compbio.ucsd.edu). These include methods on utilizing cloud computing resources and analysis of data from next-generation sequencing, systems biology, and microbiome.

keras-gcnn

Roto-reflection equivariant CNNs for Keras as presented in B. S. Veeling, J. Linmans, J. Winkens, T. Cohen, M. Welling. "Rotation Equivariant CNNs for Digital Pathology".

labs

Rmd source files for the HarvardX series PH525x

lncpipe

UNDER DEVELOPMENT--- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

maaper

Model-based analysis of APA using 3' end-linked reads

matsurv

Survival analysis in MATLAB

mermaid

WebGL-based viewer for spatially-resolved transcriptomics data

metagene-maker

makes metagene plots for next-gen sequencing data over given regions

microarray-analysis

Materials on the analysis of microarray expression data; focus on re-analysis of public data ( http://tinyurl.com/cruk-microarray)

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data