calico/hackett-doomics

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R
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MIT License
Created over 1 year ago
Updated about 1 year ago

calico/hackett-doomics

calico

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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.

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

scBasset

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

Jupyter Notebook

solo

software to detect doublets

borzoi

RNA-seq prediction with deep convolutional neural networks.

scnym

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

baskerville

Machine learning methods for DNA sequence analysis.

spatial_lda

Probabilistic topic model for identifying cellular micro-environments.

velodyn

Dynamical systems methods for RNA velocity analysis

scmmd

Maximum mean discrepancy comparisons for single cell profiling experiments

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

2019_murine_cell_aging

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

rDNAcn

Jupyter Notebook

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

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/

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.

Senescence_CD45

Jupyter Notebook

borzoi-paper

Analyses related to the Borzoi paper.

Jupyter Notebook

do_qtl

clamr

Calico Lipidomics and Metabolomics R Core Functions

hendrickson_2017_supplement

Supplemental material for the Hendrickson et. al 2017 paper.

testrepo1234

DISH