stachyris

gglabeller

Shiny gadget for labeling points on ggplot

github-stats

Better GitHub statistics images for your profile, with stats from private repos too

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

bird_genomics_review

Repository accompanying review in avian genomes by Bravo et al.

mitogenomes

Small pipeline to generate mitogenomes from short reads using NOVOPlasty

tutorial-qgis-maxent

A short tutorial for creating a species distribution model using QGIS, R, and MaxEnt.

melospiza-melodia-phenotype

Script to analyze phenotypic change

BiodiversityDataWrangling

Materials from the macroevolution module of the workshop "Biodiversity data wrangling: Linking large phylogenies with species traits and ecologies" offered at Botany 2022.

hirundo_speciation_genomics

Hirundo speciation genomics

mop

Simple tool for capturing alignment regions with sufficient quality for genotyping.

popsize

Snakemake module for the snpArcher pipeline for pop. size change inference.

Variant_Calling_Nextflow_pipeline

Pipeline for SNP Calling Created in Nextflow management system for purposesof testing the advantages of managed systems vs native applications in variant calling. The paper created and published one day is titled "NextFlow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data"

bio_utils

General utilities, functions, and to-dos for single-cell, spatial transcriptomic, and other bioinformatics analyses. Some functions and utilities may be geared towards usage within Mount Sinai's Minerva HPC infrastructure.

fcid

VCF2PCACluster

A new simple and efficient software to PCA and Cluster For popolation VCF File

tutorials

Tutorials on evolutionary genomics

gatk-snp-calling

Full GATK SNP calling pipeline

FSJ-genome

minipileup

Simple pileup-based variant caller

shinyCircos

an R/shiny application for creation of Circos plot interactively

Circos-Pipeline

circos pipeline

BOW_Quiz

RepeatModeler

De-Novo Repeat Discovery Tool

GenomeAnnotation

Various scripts that I have created that are useful for genome annotation (repeats & proteins)

ntSynt

Detecting multi-genome synteny using minimizer graph mapping

transanno

accurate LiftOver tool for new genome assemblies

GenomeAnnotation_Workshop

Materials for genome annotation sessions at the WORKSHOP ON GENOMICS, CESKY KRUMLOV

P_viridis_assembly

allele_stats

A program to calculate U20, U50, and Q95 statistics from VCF files

Genome_assembly_annotation

Scripts and pipeine for Genome_assembly_annotation