Pinned Repositories
0031_Coral_genomes
Basic analysis of available coral genomes
0032_Coral_genomes_analysis
Analysis of dark genes in coral genome and transcriptome datasets
agnostos-wf
Annotate_GOterms_from_BLAST
Annotate sequences with GOterms using BLAST
Calculate_Microbial_Diversity
R Scripts to calculate microbial diversity
Dinoflagellate_Annotation_Workflow
Dinoflagellate Annotation Workflow
Genotype_Samples
Snakemake workflow to genotype any type of NGS sample
Montipora_capitata_multi-omics_data_correlation_comparison
Code associated with the analysis of the correlation between multi-omics data generated from Montipora capitata
timothystephens.github.io
Personal website
Utils
A set of helpful scripts and tools for day-to-day bioinformatics tasks
TimothyStephens's Repositories
TimothyStephens/Dinoflagellate_Annotation_Workflow
Dinoflagellate Annotation Workflow
TimothyStephens/Genotype_Samples
Snakemake workflow to genotype any type of NGS sample
TimothyStephens/Utils
A set of helpful scripts and tools for day-to-day bioinformatics tasks
TimothyStephens/Annotate_GOterms_from_BLAST
Annotate sequences with GOterms using BLAST
TimothyStephens/Montipora_capitata_multi-omics_data_correlation_comparison
Code associated with the analysis of the correlation between multi-omics data generated from Montipora capitata
TimothyStephens/timothystephens.github.io
Personal website
TimothyStephens/0031_Coral_genomes
Basic analysis of available coral genomes
TimothyStephens/0032_Coral_genomes_analysis
Analysis of dark genes in coral genome and transcriptome datasets
TimothyStephens/agnostos-wf
TimothyStephens/Calculate_Microbial_Diversity
R Scripts to calculate microbial diversity
TimothyStephens/ColabFold_Utils
Utility Scripts for processing results from ColabFold
TimothyStephens/containerize-conda
Turn an existing conda environment into a Singularity container
TimothyStephens/Coverage_Quant
Snakemake workflow to quantify sample coverage across a set of reference genomes/MAGs
TimothyStephens/Expression_Quant
Snakemake workflow to automatically quantify gene expression with Salmon using local and SRA samples
TimothyStephens/ExtractUTRs
Predict and extract UTRs from transcripts
TimothyStephens/ExUTR
ExUTR is a practical and powerful tool that enables rapid genome-wide 3'-UTR prediction from massive RNA-Seq data
TimothyStephens/Hawaiian_coral_genomes_comparison_2022
Analysis and results from comparisons between our Hawaiian coral genomes with published data
TimothyStephens/Kaneohe_Bay_coral_2018_PopGen
Population genetics analysis of Kaneohe Bay coral samples collected in 2018
TimothyStephens/magi
Quickly find and score consensus between metabolite identifications and gene annotations
TimothyStephens/multiWGCNA
an R package for deep mining gene co-expression networks in multi-trait expression data
TimothyStephens/naive_atlas
ATLAS - Three commands to start analyzing your metagenome data
TimothyStephens/Paulinella_micropore_KR01_pathways_analysis
Major results files produced from the analysis of the nucleotide biosynthesis, DNA replication, and histidine metabolism pathways in Paulinella micropore KR01.
TimothyStephens/Paulinella_spliced_leader_sequence
Scripts for the analysis of the Paulinella spliced leader sequence using RNA-seq data and focusing on the KR01 isolate.
TimothyStephens/R_Shiny_Examples
R Shiny Examples
TimothyStephens/singularity-rstudio
A Singularity image definition file built on top of the Ubuntu 20.04 docker image with R, RStudio Server, and additional linux dependencies for common R packages installed.
TimothyStephens/snakemake-example
RNA-Seq Snakemake example with Jekyll homepage creation
TimothyStephens/TF-IDF
Provide the source code of TF-IDF program
TimothyStephens/veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes