nrminor

oneroof

Base-, Variant-, and Consensus-calling under One Proverbial Roof. Work in progress!

alltheFreyjas

A simple Nextflow wrapper that tells Freyja to do all the things

destroy_ds_stores

dds: quickly remove all those pesky .DS_Store files in the current working directory or recursively in the current directory and all subdirectories

embl-my-gbk

Convert a Genbank file with many extraneous Geneious annotations to EMBL format (even with of strict requirements as IPD)

ALPINE

Anachronistic Lineage and Persistent INfection Explorer

ALPINE-core

Implementation of ALPINE components in Rust

Amplityper

PCR Amplicon-driven Haplotype Phasing

give-a-sheet

Auto-generate type-validated, error-free input samplesheets for the nf-core pipeline you want to run. Pipeline support is limited at this stage, but more pipelines will be added in the future.

hash-browns

Metagenomic read classification well done.

nf-RASH

Take PacBio HiFi and Nanopore reads and perform de novo assembly on specific regions of the genome—or the whole thing!

amplicon-tk

A (work-in-progress) Command Line and Python Interface for Amplicon-Aware FASTQ Operations

BHasher.jl

Embarrassingly parallel checksums on large batches of files in pure Julia

checkle

Extremely fast checksum runner for arbitrarily large batches of files (WIP)

cline-cutter

Stress-testing genomic cline models with spatially explicit downsampling

filter_vcf_and_cadd_scores

Bespoke Python module for filtering a multi-sample VCF to a subset of individuals and then doing the same for CADD Scores

IPD-ref-generator

Workflow for generating useful immunological gene allele databases

letmeknow

Wrap any command with lmk to get notification banners emails, or texts on exit code 0 (WIP)

lgc

Let's Get Coding! A command line tool that creates template files and configures a development environment for projects in a variety of languages (work in progress!)

MACIC

Multiple Allelic Comparison to Identify Candidate genes

mlxai-2024-team-landrum-song

My code for the NCBI Codeathon "Building Transparent ML/AI Solutions to Advance Biological Research"

my-bioinformatics-stack

Tools for configuring my bioinformatics stack on a new machine

nf-tui

A Terminal User Interface (TUI) for configuring an arbitrarily complicated Nextflow pipeline. Work in progress!

nrminor

nrminor-stats

Github stats for nrminor

PeakBagger

Scripts and notebooks for exploring results from the ALPINE pipeline

py-rosalind-solutions

Repo for my solutions to Rosalind Bioinformatics Problems

SARS2-clade-spike-diffs

Plot spike differences among SARS-CoV-2 Pango clades

sort-and-assemble

TractorBeam

An infrastructure for transferring files to and from an HPC cluster, running command(s), and collecting results, written in Julia.

viral-saltations-in-silico

Tracking viral genomic evolution in silico in search of the mechanisms behind SARS-CoV-2 Saltatory Lineages