mattgalbraith

BaSH_seq

This pipeline processes high-throughput sequencing data (PE/SE) through QC,trim/filter,alignment,counting etc via sequential stages, with individual samples run in parallel via submission to a Slurm queue.

hisat2-docker-singularity

Build Docker container for HISAT2 and (optionally) convert to Apptainer/Singularity.

homer-docker-singularity

Build Docker container for Homer software and optionally convert to Singularity/Apptainer for running on HPC system

INCLUDE_examples

Example R scripts for analysis of INCLUDE data in CAVATICA

Rproject_template

Template files and directories for R projects

mattgalbraith/BaSH_seq

This pipeline processes high-throughput sequencing data (PE/SE) through QC,trim/filter,alignment,counting etc via sequential stages, with individual samples run in parallel via submission to a Slurm queue.

mattgalbraith/hisat2-docker-singularity

Build Docker container for HISAT2 and (optionally) convert to Apptainer/Singularity.

mattgalbraith/INCLUDE_examples

Example R scripts for analysis of INCLUDE data in CAVATICA

mattgalbraith/Rproject_template

Template files and directories for R projects

mattgalbraith/rseqc-docker-singularity

Build Docker container for RseQC and (optionally) convert to Apptainer/Singularity.

mattgalbraith/homer-docker-singularity

Build Docker container for Homer software and optionally convert to Singularity/Apptainer for running on HPC system

mattgalbraith/salmon-docker-singularity

Build Docker container for Salmon software and optionally convert to Singularity/Apptainer for running on HPC system

mattgalbraith/bbtools-docker-singularity

Build Docker container for BBTools and (optionally) convert to Apptainer/Singularity.

mattgalbraith/bowtie2-docker-singularity

Build Docker container for Bowtie 2 and (optionally) convert to Apptainer/Singularity.

mattgalbraith/bwa-docker-singularity

Build Docker container for BWA and (optionally) convert to Apptainer/Singularity.

mattgalbraith/cellranger-docker-singularity

Build Docker container for Cell Ranger and (optionally) convert to Apptainer/Singularity.

mattgalbraith/eautils-docker-singularity

Build Docker container for ea-utils and (optionally) convert to Apptainer/Singularity.

mattgalbraith/fastqc-docker-singularity

Build Docker container for FastQC software and (optionally) convert to Apptainer/Singularity.

mattgalbraith/fastqscreen-docker-singularity

Build Docker container for FastQ Screen software and (optionally) convert to Apptainer/Singularity.

mattgalbraith/fastxtoolkit-docker-singularity

Build Docker container for FASTX Toolkit and (optionally) convert to Apptainer/Singularity.

mattgalbraith/htseq2-docker-singularity

Build Docker container for HTSeq and (optionally) convert to Apptainer/Singularity

mattgalbraith/Kids-First-Elements-of-Style-Workflow-Creation-Maintenance

mattgalbraith/multiqc-docker

mattgalbraith/multiqc-docker-singularity

Build Docker container for MultiQC and (optionally) convert to Apptainer/Singularity.

mattgalbraith/picard-docker-singularity

Build Docker container for Picard Tools and (optionally) convert to Apptainer/Singularity.

mattgalbraith/presentationsR

Physical activity presentation by Brian Helsel

mattgalbraith/qiime-docker-singularity

Build Docker container for Qiime and (optionally) convert to Apptainer/Singularity.

mattgalbraith/qiime2-docker-singularity

Build Docker container for qiime2 and (optionally) convert to Apptainer/Singularity.

mattgalbraith/R-builder-sif

mattgalbraith/samtools-docker

Build a Container for samtools v1.15.1

mattgalbraith/samtools-docker-singularity

Build Docker container for Samtools software and (optionally) convert to Apptainer/Singularity

mattgalbraith/singularity-docker

Build Docker container for Apptainer/Singularity software

mattgalbraith/subread-docker-singularity

Build Docker container for Subread package and (optionally) convert to Apptainer/Singularity.

mattgalbraith/tidyHeatmap

Draw heatmap simply using a tidy data frame

mattgalbraith/tophat2-docker-singularity

Build Docker container for TopHat2 and (optionally) convert to Apptainer/Singularity.