NagaComBio

smvplot

smvplot is a cmd line python tool to generate IGV-like screenshots.

TiNDA

Tumor in normal detection

learning_ml_statistics

Learning ML with different data sets

ACEseqWorkflow

Allele-specific copy number estimation with whole genome sequencing

AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs.

BioMine

Bioinformatics data-mining

CharGer

Characterization of Germline variants

clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.

compgenomr_book

COWorkflowsBasePlugin

A basic Roddy plugin for computational oncology workflows

cv

My CV built using RMarkdown and the pagedown package.

docker-annotsv-cwl

Docker container for running AnnotSV

docker_flask

A demo flask app in docker

docker_test

A docker image for the ML

GermlineSmallVariantAnalysis

IndelCallingWorkflow

A Platypus-based workflow for indel calling

Karpathy_NN_Z2H

A tiny scalar-valued autograd engine and a neural net library on top of it with PyTorch-like API. Based on Karpathy's micrograd

kmodes

Python implementations of the k-modes and k-prototypes clustering algorithms, for clustering categorical data

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

NagaComBio

NagaComBio.github.io

octopus

Bayesian haplotype-based mutation calling

PlatypusGermlinePipeline

Platypus based small variant calling on a single or multiple samples setting.

python-mini-projects

A collection of simple python mini projects to enhance your python skills

Python_teaching

RNAseqWorkflow

Roddy RNA-seq Workflow Plugin

singularity_gcnvplotting

singularity_gSmVs

Singularity image with CharGer and R libraries for germline small variants workflow.

superintronic

A tidy interface for coverage analysis