Pinned Repositories
ASD-gut
ASD and American Gut studies
biom262-2016
Code and notebooks for BIOM262
bloom-analyses
cheatsheets
Quick lookup documents for commonly used tools
correlations
corrome
Benchmarking cross correlations
dsc80-fa19
DSC 80 Fall 19 Public repo
meth_mice
The specific aim of this study is to investigate the epigenetic mechanisms of methamphetamine use on the microbiome of mice and offspring. To address this hypothesis, pregnant mothers were injected with methamphetamine during pregnancy and continued until weaning of the offspring. Fecal samples were collected during this period every two days for mothers. Additionally, samples were collected every two days for three weeks post-treatment to determine if potential effects would be reversed. Fecal samples from pups born to mothers treated with methamphetamine or control mother treated with saline, were collected starting at an age of 21 days and continuing up until 41 days. Tissue samples from both mothers and offspring were collected at the end of the experiment which provides us the ability to correlate microbiome changes to neurological or immunological differences. After the microbiome data analysis, important phenotypes will be mapped with epigenetic changes in mothers and offsprings.
q2-qemistree
Hierarchical orderings for mass spectrometry data
qemistree-analyses
Analyses of metabolomics data using q2-qemistree
anupriyatripathi's Repositories
anupriyatripathi/meth_mice
The specific aim of this study is to investigate the epigenetic mechanisms of methamphetamine use on the microbiome of mice and offspring. To address this hypothesis, pregnant mothers were injected with methamphetamine during pregnancy and continued until weaning of the offspring. Fecal samples were collected during this period every two days for mothers. Additionally, samples were collected every two days for three weeks post-treatment to determine if potential effects would be reversed. Fecal samples from pups born to mothers treated with methamphetamine or control mother treated with saline, were collected starting at an age of 21 days and continuing up until 41 days. Tissue samples from both mothers and offspring were collected at the end of the experiment which provides us the ability to correlate microbiome changes to neurological or immunological differences. After the microbiome data analysis, important phenotypes will be mapped with epigenetic changes in mothers and offsprings.
anupriyatripathi/ASD-gut
ASD and American Gut studies
anupriyatripathi/biom262-2016
Code and notebooks for BIOM262
anupriyatripathi/bloom-analyses
anupriyatripathi/cheatsheets
Quick lookup documents for commonly used tools
anupriyatripathi/correlations
anupriyatripathi/corrome
Benchmarking cross correlations
anupriyatripathi/dsc80-fa19
DSC 80 Fall 19 Public repo
anupriyatripathi/q2-qemistree
Hierarchical orderings for mass spectrometry data
anupriyatripathi/empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
anupriyatripathi/genome-subsampler
anupriyatripathi/GNPS_Workflows
Public Workflows at GNPS
anupriyatripathi/GNPSDocumentation
Documentation for GNPS and related tools as written in mkdocs
anupriyatripathi/haddad_osa
joint analysis of gut microbiome and metabolome changes when host is exposed to intermittent hypoxia and hypercapnia
anupriyatripathi/matchms
Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
anupriyatripathi/mind-and-microbiome
A study to understand the role of microbiome in mental health
anupriyatripathi/mm-corr
Tools to understand correlations between microbiome and metabolome
anupriyatripathi/nbconvert
Jupyter Notebook Conversion
anupriyatripathi/nobel_loomba
anupriyatripathi/oecophylla
shotgun pipeline
anupriyatripathi/pyRetip
pyRetip
anupriyatripathi/qemistree-analyses
Analyses of metabolomics data using q2-qemistree
anupriyatripathi/Qemistree-Dashboard
Qemistree Reprocessing Dashboard from GNPS
anupriyatripathi/qiita
Qiita - A QIIME databasing effort
anupriyatripathi/snakemake_shotqual
Snakemake rules for parallel QC of shotgun data
anupriyatripathi/spec2vec_gnps_data_analysis
Analysis and benchmarking of mass spectra similarity measures using gnps data set.
anupriyatripathi/stats_microbiome
series of sessions to get up to speed with statistical concepts and tools for microbiome data analysis
anupriyatripathi/Tangram
Spatial alignment of single cell transcriptomic data.