anorris8

advanced-shiny

Shiny tips & tricks for improving your apps and solving common problems

beepr

The package that sounds as it is called.

Nephele

Nephele Pipeline Scripts

23andMe-To-YSNPs

If you have a 23andMe raw data file which contains Y-DNA data with refSNPs/RSID but not the names of Y-SNPs in ISOGG format, this tool will help you. Please note that only positions of build 37 are supported.

anorris8.github.io

Tips and tricks I have learned.

NCI60_GeneMetabolite_Data

RGEOde

The aim of the RGEOde project was to develop a bioinformatics unit that could be implemented broadly, by not requiring any computer programming experience and using free software and publically-available data. Teaching materials were designed to present the content in a tutorial, interactive fashion that appeals to multiple student learning styles. The lesson sequence builds on gene expression concepts covered in high school biology, reinforcing student comprehension through bioinformatics analysis of gene expression microarray data using the R programming language.

Answers

Random code produced to answer questions on biostars/seqanswers/etc.

biostats_exercises

cseaR

Cell type enrichment analysis borrowing functions from pSI, EWCE, and phenoTest R packages.

hmdbQuery

utilities for querying Human Metabolome Database

ilikebigmobileelementsandicannotlie

kandinsky

Turn any dataset into a Kandinsky painting

Lace

Building SuperTranscripts: A linear representation of transcriptome data

lenscleanR

Visual implementation of Monocle vignette in Shiny interactive environment

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

naniar

Tidy data structures, summaries, and visualisations for missing data

ODG

ODG: Omics Database Generator - Integration toolkit for -omics data

pheno4j

Pheno4j: a graph based HPO to NGS database

R.I.D.A.R

This little piece of code filters through all of the MS1 scans of an MGF file to identify if all of the associated reporter ions are present. If the reporter ions are present then a fold change identification is run. If the fold change is higher than the set threshold, the entire MS1 will be written to a new MGF file that decreases the search time and file size when compared to the original file. This ensures that scans that cannot be quantified are removed and the overall file is de-cluttered.

RagTag

Fast reference-guided genome assembly scaffolding

rladies_bmo

RLadies Baltimore Chapter

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

starfish

starfish: a modular toolkit for giant mobile element annotation

SVeedy

svm-r-markdown-templates

I have a suite of R Markdown templates for academic manuscripts, beamer presentations, and syllabi. I share them here.

swigg_shiny

Shiny app for visualizing genome graphs from SWIGG

tophat

Spliced read mapper for RNA-Seq

traz

workflowr

Organize your project into a research website