vsbuffalo/devnotes

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Vince Buffalo's devnotes — ½ TIL, ½ notebook

devnotes

Devnotes are notes I take during development, about development. The wiki contains random notes, tips, and tricks I've learned.

bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

Python

578

scidataflow

Command line scientific data management tool

Rust

175

granges

A Rust library and command line tool for working with genomic ranges and their data.

Rust

scythe

A 3'-end adapter contaminant trimmer

dotfiles

My dotfiles, with simple install script.

Vim Script

gmtfPDF

A Google Chrome extension that modifies journal links so they give you the F'ing PDF.

JavaScript

bioawk-tutorial

makefiles-in-bioinfo

A talk on Makesfiles in bioinformatics

qrqc

Quick Read Quality Control

gplyr

msr

Process MS results in R, in a tidy way

BioRanges

A small library for ranges/intervals, for use with genomic data.

Python

snakemake-tutorial

Snakemake tutorial materials

Python

genomap

A Rust library for storing generic genomic data by sorted chromosome name

Rust

rna-seq-example

An analysis of Arabidopsis RNA-seq data (hy5 mutant and wt, two replicates each; SRA accession SRX029582)

Shell

stanhl

Stan syntax highlighting for knitr

seqqs

seqqs is a C program/library for gathering quality statistics from sequencing data

good-news-everyone

Good news everyone! You can have Futurama in your shell again.

sam2counts

Count number of mapped reads per reference in SAM files (often for RNA-Seq experiments)

Python

slimflow

Python

findorf

ORF prediction of de novo transcriptome assemblies

Python

dev-sea-el

command line access to devtools

vincebuffalo-website

This is the source of my website

HTML

eidos.vim

A minimal syntax highlighting plugin for Vim for SLiM's edios language

Vim Script

cvtk

Jupyter Notebook

RNASeqTools

Diagnostics for doing RNA-seq in R

bamslider

Sliding windows in BAM/SAM files with Python's deques

Python

alignerviz

A simple tool to visualize sequences using Vlachos et al's technique

Python

coaljs

d3 neutral coalescent genealogies

JavaScript

git-demo

A very quick demo of Git for beginners

readphaser

experimental read phasing from HapCut

Python

remote_jupyter_py

Management of remote Jupyter sessions

Python

recmap

A command line tool and Rust library for working with recombination maps.

Rust

r-bioinfo-workshop

R/Bioinformatics Workshop

HTML

annotatr

bprime

Jupyter Notebook

tasselr

Some beta interfaces to Tassel's GBS data on HDF5

pathfindr

flowerpower

R pakage to access Parrot's FlowerPower plant sensor data

blast2cap3

A tool for merging transcriptome assemblies via protein homology

Python

genomicranges-intro

.emacs.d

My .emacs.d directory

Emacs Lisp

rivr

mll_translocation

Tools and notes for finding translocations in the human MLL gene

angsdr

load ANGSD data in R

samfilter

A tiny SAM/BAM filter

Python

TxDb.Zmays.Ensembl.AGPv2.17

Transcript database for Zea mays Ensembl AGPv2.17

ssbf

streaming sequence bloom filter

ms-ld

Example LD simulation with recombination using ms and libsequence.

C++

paradox_variation

TeX

quotes

A repository of quotes I like.

tempautocov

Code and some data to reproduce Buffalo and Coop (2019)

HTML

ProgenyArray

An R package to work with half-sib progeny array data

bioinfo-reading-list

A version of Hudon's MS that compiles on Mavericks

maf

An (experimental) mapping assessment framework

slper

hmmr

joy-of-base-graphics

toy-motif-finder

slirm

A fast way to launch slim jobs on slurm

Python

remote_jupyter

Management of remote Jupyter sessions.

Rust

bam-issorted

C++

mbenchpy

A command line benchmarking utility

Python

rna_seq_talk

mspy

Small Python library for parsing output from Hudson's MS

Python

quality-tutorial

A tutorial on how to use sequence quality improvement and assessment tools

codonstats

lifeweeks

A plot of your life's progress, in weeks

Python

eve102

zm_unique

C++

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