abakirbas

phylochemistry

R code phylochemistry

transXpressLite

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

phylochemical_mapping

tidyomics

Easily install and load packages from the tidyomcis ecosystem

plyranges

A grammar of genomic data transformation

tidyomicsBlog

the manifesto, workshops and tutorials of the tidy transcriptomics

tidySpatialWorkshop2024

Tidy genomic and transcriptomic analyses

tidy-intro-talk

Intro talk for tidyomics project

analysis_guides

10x Genomics analysis guides files

loupeR

Convert Seurat objects to 10x Genomics Loupe files.

tutorials

GenomeSkim_paper

RandomCode

skim2mito

A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from genome skims

genome_skimming_LAB

A set of scripts to analyze Illumina sequencing data to find whole mitochondrial genomes using Smithsonian's Hydra HPC

Skmer

Fast and accurate tool for estimating genomic distances between genome-skims

NGMD

NGMD is a bioinformatic tool for obtaining molecular markers based on plant organelle genes/genomes and nuclear gene sequence heterogeneity using genome skimming data.

skimming_scripts

scripts for preprocessing/analysis of genome skim data

Genome_Skimming_Workshop_LAB_2024

User_Codes

phytools

notebook-template

Template for a computational lab notebook using bookdown

joelem.github.io

Self webpage

academicpages.github.io

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

get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

genomeskim

QC and filtering of genome skims, followed by organelle assembly and/or genome analysis

RESPECT

Estimating repeat spectra and genome length from low-coverage genome skims

Core-to-Tree

myCORASON

This is a clean version of CORASON that works with genomes annotated in RAST and with genomes annotated with the tools in the FUNGIT repository. It wont drop large jobs on thousands of PKSs and NRPSs in fungal and bacterial genomes and in general for long sequences It uses mafft to make alignments, iqtree to make phylogenies and it wont stop if there is no core

blastin.pl

A simple script to run blast in multiple genomes and pull and pool the sequences in a file

download_genomes.sh

A bunch of scripts to download genomes (contigs, genes, proteomes) from the genbank ftp, a OsX compatible (it has some different bash commands :S) version included