• Lab static site

    CSS Updated Sep 5, 2018
  • Code used to generate the motif scraper paper

    Makefile MIT Updated May 21, 2018
  • Tool for finding matches to degenerate sequence motifs in FASTA files.

    Python 3 2 MIT Updated May 16, 2018
  • Styles I've used for NIH grant applications

    MIT Updated Feb 7, 2018
  • Compilation of R heatmap functions.

    HTML 9 2 MIT Updated Apr 28, 2017
  • Compare the read ids between two Illumina FASTQ or SCARF files to confirm reads are in sync.

    C++ GPL-3.0 Updated Dec 21, 2016
  • Python MIT Updated Oct 5, 2016
  • Python package to identify NGGNGG Cas9 gRNA sites in any indexed FASTA file.

    Python 2 1 MIT Updated Jul 6, 2016
  • Repository for data and scripts associated with manuscript

    R Updated Mar 7, 2016
  • MIT Updated Aug 3, 2015
  • Simple python script for converting a valid, multi-sample VCF file into a SNPduo compatible format.

    Python 2 GPL-3.0 Updated Mar 23, 2015
  • 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.

    R Updated Feb 23, 2015
  • Illumina FASTQ files as input and splits into individual indexed samples.

    Python GPL-3.0 Updated May 13, 2014
  • Python script for demultiplexing single-end sequencing into individual FASTQ files by index.

    Python GPL-3.0 Updated Apr 30, 2014
  • Really hacky way to remove adapters from NGS while keeping reads in order. Recommend alt strategy with cutadapt instead.

    1 GPL-3.0 Updated Oct 10, 2013
  • C++ method to convert ILMN+64 files between SCARF and FASTQ formats.

    C++ GPL-3.0 Updated Sep 9, 2013
  • 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.

    R Updated Jul 17, 2013
  • Simple program that converts FASTQ files in Solexa quality offset (QUAL+64) to a FASTQ file with Phred/Sanger offset (QUAL+33).

    C++ 1 Updated Jul 17, 2013
  • 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.

    C++ 1 Updated Jul 17, 2013

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