abakirbas

myCORASON

An alternative Version of corason with better phylogenetic trees and other features, flexible and tweakeale, for in house running, less dependencies

fun-git

A set of tools to take fungal genomes mine them for natural products, compare them using phylogenomics, cores, pangenomes. Fun As in Fungi

kew-huddle-presentation

Basic presentation about ML and plants

kewr

R Package to Access Kew Data APIs

afin

Assembly finishing program designed to perform seed based microassembly on Plastome output from a de Bruijn graph assembler.

Fast-Plast

Automated de novo assembly of whole chloroplast genomes.

PhyloHerb

PHYLOgenomic analysis pipeline for HERBarium specimens

Herbarium_Genomics

Repository for various scripts and databases used for herbarium genomics.

proActiv

Estimation of Promoter Activity from RNA-Seq data

awesome-nanopore

A curated list of awesome nanopore analysis tools.

scPred

scPred package for cell type prediction from scRNA-seq data

Nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

liger

R package for integrating and analyzing multiple single-cell datasets

al-folio

A beautiful, simple, clean, and responsive Jekyll theme for academics

samuel-marsh

Repository for personal website. Made using postcards R package.

seurat-wrappers

Community-provided extensions to Seurat

seurat

R toolkit for single cell genomics

hdWGCNA

High dimensional weighted gene co-expression network analysis

MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline

bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

cloud_computing_resources

scATACseq-analysis-notes

my notes for scATACseq analysis

scATACutils

R/Bioconductor package for working with 10x scATACseq data

awesome_spatial_omics

tools and notes for spatial omics

compbio_tutorials

My youtube programming scripts

machine-learning-resource

CUT-RUNTools-2.0

CUT&RUN and CUT&Tag data processing and analysis

docker_config

A repo for dockerfiles for various NGS analyses

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis