JasonCharamis

ARuS

Snakemake pipeline for running automated RNAseq analysis, from fastq reads to Differential Expression (DE) analysis. The latest version includes rules for post-DE annotation of genes, including annotation and/or orthology results.

CWL-workflow-for-single-cell-RNAseq-analysis

CWL workflow for single-cell RNAseq data analysis using CellRanger or STARsolo. Performs initial steps from read trimming to generating the count matrix, as well as QC, normalization, feature selection, dimensionality reduction, clustering and marker gene detection.

PhyloSuite

Suite of tools that provide a unified framework of analyzing, manipulating and visualizing phylogenetic data.

AVC

Basic-functional-annotation-using-Snakemake

This is an automated Snakemake workflow for basic functional annotation of proteomes using hmmsearch and DIAMOND against Pfam and SwissProt respectively.

ComplexHeatmap

Library for constructing multi-level heatmap figures using the ComplexHeatmap packages.

EGGNOG-functional-annotation-using-Snakemake

Snakemake workflow for functional annotation using eggNOG mapper v2

GFF3lib

Library for efficiently parsing and manipulating gff3 files.

RAxML-NG-and-Friends

Automated maximum likelihood (ML) phylogenetic analysis using RAxML-NG and the associated tools. Provides much more accurate results than IQ-TREE based phylogenies.

SandFlyComparativeGenomics

Source code for the manuscript of Charamis et al. (2024)

UpSetPlot

ETElib

Python library for efficient tree manipulation and visualization using ETE3 (http://etetoolkit.org/)

FastaLib

Custom Python library for parsing and manipulating fasta files.

FMT6lib

Custom Python library for manipulating the most common blast output (fmt6).

gggenomes_lib

Library for visualizing genome clusters using the gggenomes package.

QuteS

Snakemake workflow for quantifying transcript expression using Salmon (QuteS) in the mapping-based mode.

SCA

R library for running scRNAseq analysis using Seurat.

Snakemake-workflow-for-IQ-TREE-based-phylogenetic-analysis

Snakemake pipeline for running fast maximum likelihood phylogenetic analyses using IQ-TREE2. Works well for easy-to-analyze datasets.

Snakemake_utils

Library of functions for automating various Snakemake tasks, such as identifying the relative and absolute paths of config files

useful_scripts

Collection of useful scripts for everyday tasks.

ViolinPlots

Library for constructing high-quality violin plots.

ViS

Snakemake pipeline for variant identification from RNAseq data