surh

@TheFraserLab Stanford University

Pinned Repositories

AMOR
Abundance Matrix Operations in R
Language:R2 2 303
AMORglmnet
glmnet model on Dataset objects
Language:R1 2 00
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.
Language:R1 1 00
grins
Code for the manuscript describing discovery and distribution of GRINS in bacteria.
Language:Python1 3 120
HMVAR
Human Microbiome Variant Analysis in R
Language:R1 2 340
pbi
Microbiome analysis for phosphate-defense interaction
Language:R4 2 42
PGCA
Plate Growth Curve Analysis
Language:R0 2 00
RosetteDetector
Rosette Detection with SVM
Language:R0 2 60
scip_barplot
Workshop materials for SFSU SCIP 2022.
Language:HTML9 1 07
wheelP
Designing synthetic bacterial communities for predictable plant phenotypes
Language:R0 2 50

surh's Repositories

surh/scip_barplot
Workshop materials for SFSU SCIP 2022.
Language:HTML9 1 07
surh/pbi
Microbiome analysis for phosphate-defense interaction
Language:R4 2 42
surh/AMOR
Abundance Matrix Operations in R
Language:R2 2 303
surh/grins
Code for the manuscript describing discovery and distribution of GRINS in bacteria.
Language:Python1 3 120
surh/HMVAR
Human Microbiome Variant Analysis in R
Language:R1 2 340
surh/Rmarkdown_workshop
Language:HTML1 1 03
surh/SeqTools
Sequence utilities
Language:Perl1 2 0
surh/wheelP
Designing synthetic bacterial communities for predictable plant phenotypes
Language:R0 2 50
surh/alnnotator
Annotate multiple sequence alignments with domain information
Language:R
surh/Anchurus
Analyzing SNPs in metagenomes
Language:Jupyter Notebook1 9
surh/ANCOM
R scripts for Analysis of Composition of Microbiomes (ANCOM).
Language:R0 0
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
Language:JavaScript1 0
surh/checkm_batch
Language:Nextflow2 0
surh/crn
Analysis of community reaction norms
surh/hct
Language:R1 0
surh/HGTector
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
Language:Python
surh/inStrain
Bioinformatics program inStrain
Language:Python1 0
surh/maia-chess
Maia is a human-like neural network chess engine trained on millions of human games.
Language:Python0 0
surh/micropopgen
Scripts and utilities used @TheFraserLab
Language:Jupyter Notebook1 10
surh/nextflow-patterns
General nextflow patterns. Inspired by https://github.com/nextflow-io/patterns but more specific
Language:Nextflow2 0
surh/phybreak
Outbreak reconstruction with sequence data
Language:R0 0
surh/phylomut
Language:R
surh/RERconverge
Analysis of convergence between organismal traits and DNA/protein sequences
Language:R1 0
surh/run_roary
Run roary from a set of genbank files
Language:Python2 0
surh/sdm_useless_biology
Language:HTML
surh/simple-icons
SVG icons for popular brands
Language:HTML1 0
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.
Language:C++0 0
surh/syneco_sims
Diverse simulations for syncom design
1 0
surh/utils
General utilities
Language:Shell2 0
surh/vibrio_squid
Mathematical model(s) for the symbisis between Allivibrio fisheri and Euprymna scalopes
Language:R