khemlalnirmalkar
Research Scientist at Biodesign Center for Health Through Microbiomes
Arizona State University TempeTempe, Arizona, USA
Pinned Repositories
2019-19-03-Git-Workshop
amplicon_data_analysis
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
analysis_of_microbiome_community_data_in_r
This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://grunwaldlab.github.io/analysis_of_microbiome_community_data_in_r/
Data-science
Collection of useful data science topics along with code and articles
Data_Science
resources for courses, data analysis and visualizing tools in R and python
Diversity_customized
calculate different diversity indexes with customized codes
Introduction-to-Metagenomics-Summer-Workshop-2019
Data, scripts, and lectures for the Introduction to Metagenomics Summer Workshop 2019.
kraken2_classification
Snakemake workflow for metagenomic classification with Kraken2
MaAsLin2_customized
R package for multivariable association between clinical metadata and microbial meta-omics features
MiaBook
Microbiome Analysis Book
khemlalnirmalkar's Repositories
khemlalnirmalkar/Data-science
Collection of useful data science topics along with code and articles
khemlalnirmalkar/microeco_microbiotaDataAnalysis
An R package for data analysis in microbial community ecology
khemlalnirmalkar/AlexMohr_GM-Remodeling-IF-ProteinPacing-vs-CaloricRestriction
paper code from https://doi.org/10.1038/s41467-024-48355-5 Alex-Mohr n Corrie Whisner, intermittent fasting versus continuous caloric restriction
khemlalnirmalkar/AncientMicrobiome_GoodFigures
ancient oral microbiomes with some good taxonomy figures
khemlalnirmalkar/ANCOMBC
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
khemlalnirmalkar/ASD_multi-kingdom_diagnosis
codes from paper https://www.nature.com/articles/s41564-024-01739-1
khemlalnirmalkar/awesome-shiny-extensions
🐝 Awesome R packages that offer extended UI or server components for the R web framework Shiny
khemlalnirmalkar/birdman-differential-analyses
differential analyses tool from Knight lab
khemlalnirmalkar/EasyPubPlot
Shiny app to easily create publishable plots for scientific papers
khemlalnirmalkar/Efficient_Python_tricks_and_tools_for_data_scientists
Efficient Python Tricks and Tools for Data Scientists
khemlalnirmalkar/FEAST_sourceTracker
Fast expectation maximization for microbial source tracking
khemlalnirmalkar/FunOMIC
Fungal shotgun metagenomic profiling; taxonomic and functional
khemlalnirmalkar/GibbonsLab_Generally-Healthy-Cohort-BMF
Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.
khemlalnirmalkar/GibbonsLab_tools
R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
khemlalnirmalkar/graphlan_diet_associated_species
https://www.cell.com/cell-reports/fulltext/S2211-1247(24)01418-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124724014189%3Fshowall%3Dtrue
khemlalnirmalkar/Important-links-for-Data-analysis
codes for data analyses, manipulation and figures
khemlalnirmalkar/Maaslin3
deveolpmental stage
khemlalnirmalkar/MGnifyR
R package for searching, downloading and analysis of EBI MGnify metagenomics data
khemlalnirmalkar/Micke_Metagenome-CoAssembly
Metagenome CoAssembly scripts from Michael Pavia
khemlalnirmalkar/MOFA2--MultiOmics-data-analysis
Multi-Omics Factor Analysis
khemlalnirmalkar/Multi-OMICS_repositories
link of different repositories for multi-omics data analysis
khemlalnirmalkar/nf-co.re_dataAnalyses_resource
Code and files for the main nf-core website.
khemlalnirmalkar/nicePlotsFromApaper_GutMicrobes
codes from https://www.tandfonline.com/doi/epdf/10.1080/19490976.2023.2292254?needAccess=true
khemlalnirmalkar/PacBio_pb-16S-nf
Nextflow pipeline to analyze PacBio HiFi full-length 16S data
khemlalnirmalkar/q2-ancombc
qiime2 plugin for ANCOMBC
khemlalnirmalkar/q2-fmt
Plugin for analysing the efficacy of fecal microbiota transplants
khemlalnirmalkar/Repositories4_courses_stats
links of various courses and stats in R & python
khemlalnirmalkar/Rscripts-and-hmp2-data
Omnibus and Maaslin2 Rscripts and hmp2-data for downstream analyis
khemlalnirmalkar/Tarini_NatureAgeMetaAnalysis_Codes
Codes and Data corresponding to the meta-analysis investigating age-gut microbiome interactions in seven major microbiome data repositories
khemlalnirmalkar/tempted_longiMicrobeData
this tool is to analyze longitudinal microbiome data