Pinned Repositories
MolPad
MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics
generative_review
Code accompanying "Generative Models: An Interdisciplinary Perspective"
glacier_mapping
Mapping glaciers in the Hindu Kush Himalaya, in partnership with ICIMOD.
Humanitarian-AI
Weekly humanitarian AI reading group at Mila.
interpretability_review
Code accompanying a review article on interpretability and XAI. Includes examples for both simple (sparse regression) and sophisticated (concept bottlenecks) approaches, using notebooks that can be run in a few minutes.
microbiome_plvm
Code for simulations and analysis for "Latent Variable Modeling for the Microbiome."
multimedia
multimedia is an R package for multimodal mediation analysis of microbiome data. It has been designed to help integration of relative abundance, survey, and metabolomic data through causal mediation analysis.
multitable_review
Code to accompany "Multitable Methods for Microbiome Data Integration"
treelapse
timelapse + trees = treelapse
alto
'alto' is an R package that aligns topics from different LDA models, computes metrics for quantifying the goodness of alignment, and provides visualization functions to explore the alignment and robustness of topics across environments or LDA hyper-parameters.
krisrs1128's Repositories
krisrs1128/OpioidAtlas
An interactive tool for exploring and visualizing opioid consumption around the world from 1989-2013, based on data from the International Narcotics Control Board (INCB).
krisrs1128/readings
Attempts to implement things I'm reading.
krisrs1128/microbiome_regime_detection
krisrs1128/100_days
some random d3 experiments
krisrs1128/mvarVisApp
Very preliminary experiment with using mvarVis in a Shiny app.
krisrs1128/.emacs.d
krisrs1128/BIOME
BIOinformatics for MEtabarcoding
krisrs1128/boot_expers
Some bootstrapping experiments.
krisrs1128/edward
A library for probabilistic modeling, inference, and criticism. Deep generative models, variational inference. Runs on TensorFlow.
krisrs1128/example-models
Example models for Stan
krisrs1128/ggscaffold
Scaffolding for verbose ggplot figures.
krisrs1128/knockoff_expers
krisrs1128/map_labels
A preliminary study on how different strong and weak forms of supervision compare in humanitarian mapping efforts.
krisrs1128/microbiome_multitable
krisrs1128/microbiome_pred
Experiments with prediction pipeline for microbiome data.
krisrs1128/modeldb
A system to manage machine learning models
krisrs1128/my-spacemacs
krisrs1128/nmfSim
Helper functions for running NMF simulations.
krisrs1128/phd_thesis
krisrs1128/plant_trace_analysis
Quantitative descriptions of plant responses to wounding.
krisrs1128/simFuns
krisrs1128/SLURMHelpers
Because I always panic whenever I need to parallelize an experiment on Sherlock.
krisrs1128/stamps
Course materials for STAMPS @ MBL
krisrs1128/stan_exercises
krisrs1128/toggl_analyze
Analyzing csvs from toggl.
krisrs1128/tree_ts_sim
Functions for simulating time series on trees.
krisrs1128/treelapse_notes
krisrs1128/unsupervised_prob
Notes for probabilistic unsupervised modeling of the microbiome
krisrs1128/updateR
update your R version in a breeze ( on OSX)
krisrs1128/well_microbiome_expers
General exploration / experiments with the WELL dataset.