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.github

Repository that stores default .github files

2019_murine_cell_aging

Tools associated with the Calico Murine Aging Cell Atlas, Kimmel 2019 et. al., Genome Research

aac_scoring

Map DEXA images from UKBB dataset to abdominal aortic calcification scores

adaptive_interference_inference

A mathematical optimization problem, inspired by an apparent paradox in the physics of optical measurement. Read the micro-publication here: https://calico.github.io/adaptive_interference_inference

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

baskerville

Machine learning methods for DNA sequence analysis.

bayesian_survival_analysis

borzoi

RNA-seq prediction with deep convolutional neural networks.

borzoi-paper

Analyses related to the Borzoi paper.

calicolipidlibrary

In silico Lipid fragmentation patterns

catnap

CATNAP-related code

claman

Calico Lipidomics and Metabolomics (CLaM) Analysis provides a suite of functions which support data manipulation, statistical analysis and visualizations of mzrollDB files created by MAVEN.

clamdb

CLaM Database Management

clamqc

Quality Control for open_CLaM pipeline processing methods.

clamr

Calico Lipidomics and Metabolomics R Core Functions

dish

do_bwd

Python implementation of extracting body weight dynamics in diversity outbred mice using ARHMM.

do_qtl

elegans-observatory

elmaven

LC-MS data processing engine for large-scale metabolomic experiments.

hackett-doomics

Plasma multiomics (metabolites + lipids + proteins) from the SHOCK cohort of Diverse Outcross (DO) mice. 110 mice were longitudinally profiled at 8, 14, and 20 months and molecules abundances were compared to their age and natural lifespan. This repository supports a TO-BE-RELEASED publication interrogating this dataset.

hendrickson_2017_supplement

Supplemental material for the Hendrickson et. al 2017 paper.

impulse

Fit phenomenological sigmoid and impulse curves with priors to improve interpretability

mstrawler

open_clam

open-source version of mass_spec

quahog

Pipeline-associated functions for CLaM searches

rdnacn

remote_refocus

A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://calico.github.io/remote_refocus/

rescan_line_sted

A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://calico.github.io/rescan_line_sted

romic

romic represents high-dimensional measurements by persistently tracking features, samples, and measurements as a dataset is modified and reformatted. It provides a suite of functions that build on this framework to support data analysis and visualization. These functions are combined into shiny apps tailored to exploratory data analysis.