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