Pinned Repositories
AMOR
Abundance Matrix Operations in R
AMORglmnet
glmnet model on Dataset objects
delta_statistic
Codes for calculating delta, a phylogenetic analog of the Shannon entropy for measuring the degree of phylogenetic signal between a categorical trait and a phylogeny.
grins
Code for the manuscript describing discovery and distribution of GRINS in bacteria.
HMVAR
Human Microbiome Variant Analysis in R
pbi
Microbiome analysis for phosphate-defense interaction
PGCA
Plate Growth Curve Analysis
RosetteDetector
Rosette Detection with SVM
scip_barplot
Workshop materials for SFSU SCIP 2022.
wheelP
Designing synthetic bacterial communities for predictable plant phenotypes
surh's Repositories
surh/scip_barplot
Workshop materials for SFSU SCIP 2022.
surh/pbi
Microbiome analysis for phosphate-defense interaction
surh/AMOR
Abundance Matrix Operations in R
surh/grins
Code for the manuscript describing discovery and distribution of GRINS in bacteria.
surh/HMVAR
Human Microbiome Variant Analysis in R
surh/Rmarkdown_workshop
surh/SeqTools
Sequence utilities
surh/wheelP
Designing synthetic bacterial communities for predictable plant phenotypes
surh/alnnotator
Annotate multiple sequence alignments with domain information
surh/Anchurus
Analyzing SNPs in metagenomes
surh/ANCOM
R scripts for Analysis of Composition of Microbiomes (ANCOM).
surh/awesome-selfhosted
A list of Free Software network services and web applications which can be hosted locally. Selfhosting is the process of hosting and managing applications instead of renting from Software-as-a-Service providers
surh/checkm_batch
surh/crn
Analysis of community reaction norms
surh/hct
surh/HGTector
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
surh/inStrain
Bioinformatics program inStrain
surh/maia-chess
Maia is a human-like neural network chess engine trained on millions of human games.
surh/micropopgen
Scripts and utilities used @TheFraserLab
surh/nextflow-patterns
General nextflow patterns. Inspired by https://github.com/nextflow-io/patterns but more specific
surh/phybreak
Outbreak reconstruction with sequence data
surh/phylomut
surh/RERconverge
Analysis of convergence between organismal traits and DNA/protein sequences
surh/run_roary
Run roary from a set of genbank files
surh/sdm_useless_biology
surh/simple-icons
SVG icons for popular brands
surh/SLiM
SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.
surh/syneco_sims
Diverse simulations for syncom design
surh/utils
General utilities
surh/vibrio_squid
Mathematical model(s) for the symbisis between Allivibrio fisheri and Euprymna scalopes