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/woltka
Web of Life Toolkit App
khemlalnirmalkar/binarena
khemlalnirmalkar/biom-format
The Biological Observation Matrix (BIOM) Format Project
khemlalnirmalkar/Bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
khemlalnirmalkar/EnrichmentMapApp
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
khemlalnirmalkar/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
khemlalnirmalkar/FindFungi_shotgun
A pipeline for the identification of fungi in public metagenomics datasets
khemlalnirmalkar/gephi
Gephi - The Open Graph Viz Platform
khemlalnirmalkar/ggpubr
'ggplot2' Based Publication Ready Plots
khemlalnirmalkar/halla
Hierarchical All-against-All association testing is designed as a command-line tool to find associations in high-dimensional, heterogeneous datasets.
khemlalnirmalkar/Heatmapper
to make different kind of heatmap http://www.heatmapper.ca/expression/
khemlalnirmalkar/hierarchical-models
A Visual Introduction to Hierarchical Modeling
khemlalnirmalkar/iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
khemlalnirmalkar/interproscan
khemlalnirmalkar/jupyterlab
JupyterLab computational environment.
khemlalnirmalkar/Metaboverse
Visualizing and Analyzing Metabolic Networks
khemlalnirmalkar/Metagen-FastQC
Wrapper to clean metagenomic reads
khemlalnirmalkar/metagenomics_summer_school
Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in December
khemlalnirmalkar/metagenomics_workflows
Workflows for metagenomic sequence data processing and analysis.
khemlalnirmalkar/metamicrobiomeR
An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models
khemlalnirmalkar/MetENP
khemlalnirmalkar/multiomic-cooccurrences
khemlalnirmalkar/pingouin
Statistical package in Python based on Pandas
khemlalnirmalkar/python-for-newbies
A guide to Python for absolute beginners
khemlalnirmalkar/Python-minibook-2nd-code
Code of the IPython Minibook, 2nd edition (2015)
khemlalnirmalkar/q2-micom
A Qiime plugin for MICOM.
khemlalnirmalkar/shell-novice
The Unix Shell
khemlalnirmalkar/statannot
add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot
khemlalnirmalkar/statsmodels
Statsmodels: statistical modeling and econometrics in Python
khemlalnirmalkar/tests-as-linear
Common statistical tests are linear models (or: how to teach stats)