calico/baskerville

Machine learning methods for DNA sequence analysis.

Language: Python - Size: 17.8 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 21 - Forks: 3

calico/impulse

Fit phenomenological sigmoid and impulse curves with priors to improve interpretability

Language: R - Size: 1.37 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 10 - Forks: 2

calico/basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

Language: Python - Size: 152 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 375 - Forks: 119

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.

Language: R - Size: 10.8 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 2 - Forks: 0

calico/borzoi-paper

Analyses related to the Borzoi paper.

Language: Jupyter Notebook - Size: 144 MB - Last synced: 25 days ago - Pushed: 27 days ago - Stars: 0 - Forks: 0

calico/borzoi

RNA-seq prediction with deep convolutional neural networks.

Language: Python - Size: 4.15 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 57 - Forks: 5

calico/solo

software to detect doublets

Language: Python - Size: 36.4 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 77 - Forks: 13

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.

Language: R - Size: 19.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 1

calico/scmmd

Maximum mean discrepancy comparisons for single cell profiling experiments

Language: Python - Size: 20.5 KB - Last synced: about 14 hours ago - Pushed: over 2 years ago - Stars: 14 - Forks: 3

calico/ukbb-mri-sseg

UKBB MRI semantic segmentation for Abdominal Dixon and other modalities

Language: Python - Size: 44.9 KB - Last synced: 18 days ago - Pushed: 8 months ago - Stars: 9 - Forks: 6

calico/scBasset

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

Language: Jupyter Notebook - Size: 91.5 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 82 - Forks: 11

calico/AAC_scoring

Map DEXA images from UKBB dataset to abdominal aortic calcification scores

Language: Python - Size: 203 MB - Last synced: 3 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 2

calico/velodyn

Dynamical systems methods for RNA velocity analysis

Language: Python - Size: 832 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 23 - Forks: 1

calico/scnym

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

Language: Python - Size: 4.76 MB - Last synced: 20 days ago - Pushed: 6 months ago - Stars: 73 - Forks: 12

calico/spatial_lda

Probabilistic topic model for identifying cellular micro-environments.

Language: Python - Size: 10.8 MB - Last synced: about 8 hours ago - Pushed: 11 months ago - Stars: 25 - Forks: 10

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.

Language: R - Size: 192 KB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

calico/.github

Repository that stores default .github files

Size: 1.95 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

calico/msTrawler

Language: R - Size: 3.85 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

calico/elegans-observatory

Size: 5.86 KB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

calico/do_qtl

Language: Python - Size: 511 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 1

calico/DISH

Language: Python - Size: 47.2 MB - Last synced: 9 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

calico/Senescence_CD45

Language: Jupyter Notebook - Size: 43.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

calico/rDNAcn

Language: Jupyter Notebook - Size: 81.3 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

calico/testrepo1234

testing 123

Size: 1000 Bytes - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

calico/Bayesian_Survival_Analysis

Language: Python - Size: 2.94 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

calico/2019_murine_cell_aging

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

Language: Python - Size: 18.6 KB - Last synced: over 1 year ago - Pushed: about 4 years ago - Stars: 3 - Forks: 1

calico/CalicoLipidLibrary

In silico Lipid fragmentation patterns

Language: Python - Size: 273 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

calico/catnap

CATNAP-related code

Language: Python - Size: 67.4 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

calico/open_CLaM

open-source version of mass_spec

Language: Python - Size: 74.4 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

calico/quahog

Pipeline-associated functions for CLaM searches

Language: R - Size: 50.8 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

calico/clamdb

CLaM Database Management

Language: R - Size: 165 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

calico/clamr

Calico Lipidomics and Metabolomics R Core Functions

Language: R - Size: 375 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

calico/clamqc

Quality Control for open_CLaM pipeline processing methods.

Language: R - Size: 30.3 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

calico/ylmcv

Inference code for yeast lifespan machines

Language: Python - Size: 46.5 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

calico/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/

Language: Python - Size: 40.4 MB - Last synced: over 1 year ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0

calico/hendrickson_2017_supplement

Supplemental material for the Hendrickson et. al 2017 paper.

Language: Python - Size: 30.3 KB - Last synced: over 1 year ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 1

calico/stimulated_emission_imaging Fork of AndrewGYork/stimulated_emission_imaging

A scientific publication that describes experiments to explore whether stimulated emission from a pointlike emitter is distinguishable from the stimulating beam. This repository hosts everything you need to reproduce our results. Read the publication here: https://calico.github.io/stimulated_emission_imaging

Language: Python - Size: 94 MB - Last synced: over 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

calico/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

Language: Python - Size: 3.2 MB - Last synced: over 1 year ago - Pushed: almost 6 years ago - Stars: 3 - Forks: 0

calico/ElMaven Fork of ElucidataInc/ElMaven

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

Language: C++ - Size: 636 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

calico/adaptive_interference_inference Fork of AndrewGYork/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

Language: HTML - Size: 2.94 MB - Last synced: 4 months ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0