Calico

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

scBasset

Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.

solo

software to detect doublets

scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

borzoi

RNA-seq prediction with deep convolutional neural networks.

spatial_lda

Probabilistic topic model for identifying cellular micro-environments.

baskerville

Machine learning methods for DNA sequence analysis.

ukbb-mri-sseg

UKBB MRI semantic segmentation for Abdominal Dixon and other modalities

impulse

Fit phenomenological sigmoid and impulse curves with priors to improve interpretability

msTrawler

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.

AAC_scoring

Map DEXA images from UKBB dataset to abdominal aortic calcification scores

rDNAcn

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.

do_qtl

Senescence_CD45

clamr

Calico Lipidomics and Metabolomics R Core Functions

DISH

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.

testrepo1234

testing 123

Bayesian_Survival_Analysis

.github

Repository that stores default .github files

borzoi-paper

Analyses related to the Borzoi paper.

CalicoLipidLibrary

In silico Lipid fragmentation patterns

clamqc

Quality Control for open_CLaM pipeline processing methods.

elegans-observatory

open_CLaM

open-source version of mass_spec

quahog

Pipeline-associated functions for CLaM searches