Dave Carlson's repositories
RNA-Seq-saturation-curve
RNA-Seq Saturation Curve
Snakemake_diff_gene_expr
Differential Gene Expression with Snakemake
alphafold_singularity
Singularity recipe for AlphaFold
Bash-Oneliner
A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.
BayeScan
Detecting natural selection from population-based genetic data
bc_osc_qgis
Batch Connect - OSC QGIS
Brython-Editor
A Brython editor for entry-level python classes.
comparative-oenothera-transcriptomics
Repo for housings scripts and data for Oenothera comparative transcriptomics project
configs
Config files used to define parameters specific to compute environments at different Institutions
cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
Fasta-Manipulation
Python scripts for working with fasta files and other common bioinformatics formats
MPI-bioinformatics
An ever-expanding list of bioinformatics software that can be parallelized across multiple compute nodes in an HPC environment
Scripts
Misc. scripts for bioinformatics
fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nuvotrans
A nextflow pipeline for de novo transcriptome assembly
oenothera_popgenomics
Miscellaneous scripts used for conducting population genomics analysis from Oenothera data
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
SARS-CoV2-variant-calling-example
An educational variant calling example with short read Illumina data using the SARS-CoV2 genome
SBU-thesis-template
The latex template for Stony Brook University Ph.D. and MS Thesis
SHMprep_scripts
Scripts for running and testing the SHMprep IG-seq read processing tool.
Snakemake-bcftools
A snakemake variant calling pipeline using Bcftools
snakemake-GATK
A snakemake pipeline for variant calling with GATK
snakemake-trinotate
A snakemake pipeline for using Trinotate to annotate multiple transcriptomes assembled with Trinity
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
unix_tips_etc
A collection of scripts/commands for working in UNIX environments