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basic_scanpy

basic scanpy run

best-of-ml-python

🏆 A ranked list of awesome machine learning Python libraries. Updated weekly.

biotools

Bioinformatics tools used by me

brick

Python3 based pipeline constructor

cellxgene

An interactive explorer for single-cell transcriptomics data

covtest

covTest package by R Lockhart

cscipipe

Pipeline commands for CSCI

docker_r350

R version 3.5.0 for farm5

docker_scanpy

dockerised version of scanpy.

docker_spladder

Dockerise spladder

easyrun

Just a python code to submit jobs in slurm

encoded

Metadata database for ENCODE project

genvisr

Genome data visualizations

intro-machine-learning

lenhancer

Enhancer identification using LASSO

mudata

Multimodal Data (.h5mu) implementation for Python

nf-irods-to-fastq

Get CRAMs from iRODS and convert them to fastq

pairedvoting

pisan

Sanger specific pipeline for NGS

rabbitgastrulation2022

rincewind

Python3 based command center

rnamut

Robust Identification of Clinically Relevant Mutations in Acute Myeloid Leukaemia Using RNA-seq

samtools-1.9

Docker of Ubuntu:18.04 with samtools 1.9

scanpy

Single-cell analysis in Python. Scales to >1M cells.

scanpy_functions

Functions that work alongside scanpy anndata objects. Useful functions for single cell analysis

scrnaseq

Files for sc-RNASeq analysis that I find is useful

scrnaseq_dash

scvm

Supplementary tools for analysis of anndata + Scanpy scverse

scvoting

Paired-voting method

shearwater

deepSNV 1.24 running with R-3.4.0 on Ubuntu 18.06