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PyRate Public
Forked from dsilvestro/PyRatePyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
Python GNU Affero General Public License v3.0 UpdatedJun 26, 2024 -
hpc_tools Public
A collection of various HPC monitoring utility scripts
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modules Public
Forked from nf-core/modulesRepository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow MIT License UpdatedMay 14, 2024 -
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nuvotrans Public
A nextflow pipeline for de novo transcriptome assembly
Groovy MIT License UpdatedNov 30, 2023 -
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fetchngs Public
Forked from nf-core/fetchngsPipeline to fetch metadata and raw FastQ files from public and private databases
Groovy MIT License UpdatedJun 15, 2023 -
configs Public
Forked from nf-core/configsConfig files used to define parameters specific to compute environments at different Institutions
Nextflow MIT License UpdatedApr 20, 2023 -
snakemake-wrappers Public
Forked from snakemake/snakemake-wrappersThis is the development home of the Snakemake wrapper repository, see
CAP CDS UpdatedApr 5, 2023 -
alphafold_singularity Public
Forked from prehensilecode/alphafold_singularitySingularity recipe for AlphaFold
Python Apache License 2.0 UpdatedFeb 17, 2023 -
MPI-bioinformatics Public
An ever-expanding list of bioinformatics software that can be parallelized across multiple compute nodes in an HPC environment
Creative Commons Zero v1.0 Universal UpdatedAug 25, 2022 -
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oenothera_popgenomics Public
Miscellaneous scripts used for conducting population genomics analysis from Oenothera data
Python UpdatedJan 14, 2022 -
Snakemake-bcftools Public
A snakemake variant calling pipeline using Bcftools
Python UpdatedNov 10, 2021 -
SBU-thesis-template Public template
Forked from urfdvw/SBU-thesis-templateThe latex template for Stony Brook University Ph.D. and MS Thesis
TeX Other UpdatedAug 24, 2021 -
Brython-Editor Public
Forked from urfdvw/Brython-EditorA Brython editor for entry-level python classes.
HTML UpdatedJul 30, 2021 -
Repo for housings scripts and data for Oenothera comparative transcriptomics project
Python UpdatedJul 13, 2021 -
Snakemake_diff_gene_expr Public
Differential Gene Expression with Snakemake
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Fasta-Manipulation Public
Python scripts for working with fasta files and other common bioinformatics formats
Python UpdatedJul 13, 2021 -
snakemake-GATK Public
A snakemake pipeline for variant calling with GATK
Python UpdatedJul 13, 2021 -
SHMprep_scripts Public
Scripts for running and testing the SHMprep IG-seq read processing tool.
Shell UpdatedJun 30, 2021 -
An educational variant calling example with short read Illumina data using the SARS-CoV2 genome
Python UpdatedFeb 10, 2021 -
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snakemake-trinotate Public
A snakemake pipeline for using Trinotate to annotate multiple transcriptomes assembled with Trinity
Python UpdatedJan 15, 2021 -
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Bash-Oneliner Public
Forked from onceupon/Bash-OnelinerA collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.
MIT License UpdatedOct 21, 2019 -
rna-seq-star-deseq2 Public template
Forked from snakemake-workflows/rna-seq-star-deseq2RNA-seq workflow using STAR and DESeq2
Python MIT License UpdatedJul 24, 2019 -
dna-seq-gatk-variant-calling Public template
Forked from snakemake-workflows/dna-seq-gatk-variant-callingThis Snakemake pipeline implements the GATK best-practices workflow
Python MIT License UpdatedJun 25, 2019 -
cookiecutter-snakemake-workflow Public
Forked from snakemake-workflows/cookiecutter-snakemake-workflowA cookiecutter template for Snakemake workflows
Python MIT License UpdatedApr 5, 2019 -
unix_tips_etc Public
Forked from benjamincjackson/unix_tips_etcA collection of scripts/commands for working in UNIX environments
R UpdatedMar 14, 2019