Pinned Repositories
basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
baskerville
Machine learning methods for DNA sequence analysis.
borzoi
RNA-seq prediction with deep convolutional neural networks.
scBasset
Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
scmmd
Maximum mean discrepancy comparisons for single cell profiling experiments
scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
solo
software to detect doublets
spatial_lda
Probabilistic topic model for identifying cellular micro-environments.
ukbb-mri-sseg
UKBB MRI semantic segmentation for Abdominal Dixon and other modalities
velodyn
Dynamical systems methods for RNA velocity analysis
Calico's Repositories
calico/basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
calico/scBasset
Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
calico/borzoi
RNA-seq prediction with deep convolutional neural networks.
calico/solo
software to detect doublets
calico/scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
calico/baskerville
Machine learning methods for DNA sequence analysis.
calico/spatial_lda
Probabilistic topic model for identifying cellular micro-environments.
calico/ukbb-mri-sseg
UKBB MRI semantic segmentation for Abdominal Dixon and other modalities
calico/impulse
Fit phenomenological sigmoid and impulse curves with priors to improve interpretability
calico/msTrawler
calico/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.
calico/AAC_scoring
Map DEXA images from UKBB dataset to abdominal aortic calcification scores
calico/borzoi-paper
Analyses related to the Borzoi paper.
calico/rDNAcn
calico/calicolabs-piccolo
calico/catnap
CATNAP-related code
calico/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.
calico/do_qtl
calico/Senescence_CD45
calico/clamr
Calico Lipidomics and Metabolomics R Core Functions
calico/DISH
calico/ElMaven
LC-MS data processing engine for large-scale metabolomic experiments.
calico/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.
calico/testrepo1234
testing 123
calico/Bayesian_Survival_Analysis
calico/.github
Repository that stores default .github files
calico/CalicoLipidLibrary
In silico Lipid fragmentation patterns
calico/do_bwd
Python implementation of extracting body weight dynamics in diversity outbred mice using ARHMM.
calico/DRiDO_Paper_Release
calico/elegans-observatory