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Code used to generate the motif scraper paper
Tool for finding matches to degenerate sequence motifs in FASTA files.
Styles I've used for NIH grant applications
Lab static site
Compilation of R heatmap functions.
Compare the read ids between two Illumina FASTQ or SCARF files to confirm reads are in sync.
Python package to identify NGGNGG Cas9 gRNA sites in any indexed FASTA file.
Repository for data and scripts associated with manuscript
Simple python script for converting a valid, multi-sample VCF file into a SNPduo compatible format.
Repository for the web-based version / visualization engine for the SNPduoWeb tool. Designed to visualize identity-by-state in high-density snp data. Originally developed in the lab of Dr. Jonathan Pevsner at the Kennedy Krieger Institute in Baltimore. Publication PMID: 19696932.
Illumina FASTQ files as input and splits into individual indexed samples.
Python script for demultiplexing single-end sequencing into individual FASTQ files by index.
Really hacky way to remove adapters from NGS while keeping reads in order. Recommend alt strategy with cutadapt instead.
C++ method to convert ILMN+64 files between SCARF and FASTQ formats.
Functions that allow direct differential expression testing of 1 versus 1 array using the average intensities, bead count, standard errors and detection p-values. Requires beadarray.
Simple program that converts FASTQ files in Solexa quality offset (QUAL+64) to a FASTQ file with Phred/Sanger offset (QUAL+33).
Repository for the snpduo command-line tool. The tool is designed to calculate identity-by-state in large SNP genotyping datasets. Originally developed in the lab of Dr. Jonathan Pevsner at the Kennedy Krieger Institute in Baltimore. Publication PMID: 19696932.