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10genomes

These are the scripts from my phylogenetics paper. I don't think they will work as is, I just wanted to back them up. Please don't judge me for their inelegance, I made them when the only programming language I had any experience with was AWK, and not much of that.

2018-11-emborome

Training materials from the EMBO course Computational analysis of protein-protein interactions: Sequences, networks and diseases, taking place from 05 to 10 November 2018 in Rome, Italy.

aba-boolean-network-model

Code and documentation for a discrete dynamic model of ABA-induced stomatal closure.

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

agla_gb_supp-scripts

This repository contains scripts used for various sections of the paper "Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface".

alignment_filtering

Code and data for "Limited Utility of Residue Masking for Positive-Selection Inference," by SJS, ETD, COW.

altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

amanita_comparative_genomics

Companion scripts for Amanita comparative genomics paper "Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita"

amp_phase1_ra

Use single-cell transcriptomics and proteomics to study autoimmune diseases (AMP Phase I paper)

ani_analysis

annocript

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts.

annotatevariants

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

appinetwork

construction and Analysis of Protein-Protein Interactions (PPI) NETWORKS for complexes and biological processes

aspergillus_ps

In this repository I describe the workflow followed to process and analyze the data of the study "A genomic view on Aspergillus fumigatus against 18 species of the genus Aspergillus: Conservation, evolution and specific virulence genes"

awesome-hacking

A collection of various awesome lists for hackers, pentesters and security researchers

awesome-single-cell

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

b73_scripts

These are scripts that were written for work I did annotating version 4 of the maize B73 genome

bac-genomics-scripts

Collection of scripts for bacterial genomics

bacteria2go

Quick and dirty script to download and analyse bacterial genomes from NCBI

beautiful-jekyll

:sparkles: Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll

bibnet-google-scholar-scraper

binning

Code for statistical binning and related scripts

bio-pipeline

My collection of light bioinformatics analysis pipelines for specific tasks

bioinfo-tools

Collection of Python and other data analysis resources

bioinformatics

Robs General Bioinformatics Repo.... Free code for all to use

bioinformaticsdotca.github.io

Repo for student website

biotools

Scripts for CMG-Biotools

biotools-1

A list of useful bioinformatics resources

blast

A Simple Web Application Framework for PHP

blast-template

A simple template engine for PHP.