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ansible-playbook-scicore-courses-cloud

Ansible playbooks to boot resources in the cloud for the sciCORE courses

ccpca

ccPCA: contrasting clusters in PCA.

concentrictree

generation of a "beautiful" tree of life

corona_benford

coverage_viewer

interactive vizualization of overlayed coverage tracks

csv-to-openspace

helper code to go from data in a csv format to a .speck and .asset files importable in openSpace

decostar

repository for all DeCoSTAR standalone code

elasticluster

A staging area for my (larger) contributions to ElastiCluster. See http://github.com/gc3-uzh-ch/elasticluster for the real thing

encyclopedia-of-life-info-scraper

helper scripts to grab data (images, mainly) about specific species from the Encyclopedia Of Life (https://eol.org/)

fwdtreesim

Python module for simulation of forward evolution of a prokaryotic(-like) pangenome

genometrace

Code pertaining to the computation and optimization of a global score (TRACE) defined on a group of gene families associated with a species tree and with adjacencies between extant genes

integrate_tree_to_xyz

Scripts to project a tree structure in 3D from a set of coordinates of their leaves (by default 2D coordinates).

junk

tmp to play

jupyterlite_demo

mp4-video-chopper

a few python notebook to help editing mp4 video - mostly a wrapper around ffmpeg

ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

pykleebarcode

Implements methods and scripts to compute a structure matrix from a multiple sequence alignment. Th

pykleebarcode-publication-supporting-code-and-data

contains the code and data to accompany the publication of the pyKleeBarcode software (https://github.com/WandrilleD/pyKleeBarcode)

recoderlaroue

recoder des algorithmes connus en phylogénie (et autres), dans un objectif pédagogique

recphyloxml

PhyloXML inspired format to represent reconciliations

rnaseq-introduction-training

Webpage of the "Introduction to RNA-Seq: From quality control to pathway analysis - streamed" SIB course.

scdeed_python

a python implementation of the R scDEED package (https://github.com/JSB-UCLA/scDEED)

severe-neuro-covid-cross-sectional-study-etteretal2022

Computational documents of "Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study" by Etter et al. 2022

tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

training-collection

Collection of bioinformatics training materials