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orthofinder

Phylogenetic orthology inference for comparative genomics

pathweaver

A suite of tools for local haplotype reconstruction

phylopandas

Pandas DataFrames for phylogenetics

principles-of-sequence-analysis-and-phylogenetics

Materials for the ACE - Uganda course "Principles of Sequence Analysis and Phylogenetics" given in Spring 2020.

project-3

Interrogating public datasets and paths to results on COVID-19 in East Africa

pydna

Double stranded DNA & simulation of homologous recombination, Gibson assembly, cut&paste cloning in Python and Jupyter notebooks

r-toolkit-for-metagenomic-studies

R scripts for analyzing metagenomic annotations of datasets from microbial communities

r_intro

A Gentle Introduction to R, RStudio, and visualization

r_rmarkdown_shiny

This repository is meant for the R part of the EANBiT 2019 residential training

recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

rmap

Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS

rnaseq_deseq2_workshop

RNAseq workshop courses and materials

roary

Rapid large-scale prokaryote pan genome analysis

sample_db

Application for managing a sample tracking DB

sampledb-rpackage

seqr

web-based analysis tool for rare disease genomics

shahiid-s-guessing-game

README.md, makefile

shitty_contigs

Find contigs/scaffolds that may be contaminants in genomic assemblies.

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

singularity

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

snippy

:scissors: :zap: Rapid bacterial SNP calling and core genome alignments

snippy-accessory

Provides a pan-genome variant matrix from snippy-core full genome alignments

snp-slice

SNP-Slice: a Bayesian nonparametric method to resolve multi-strain infections.

spades

SPAdes Genome Assembler

statistical-testing

Training materials for Statistical Testing

tb-tad

therealmccoil

A Markov chain Monte Carlo method that estimates complexity of infection and population allele frequencies using SNP data obtained from Sequenom or similar types of SNP assays.

thursday19thmay

trends-in-prokaryote-genomics

R script for identifying trends in bacterial and archaeal genomics through number of genome sequencing projects submitted to ncbi per year.

trycycler

A tool for generating consensus long-read assemblies for bacterial genomes