99 projects
cell-neighbors
voyager-based kNN for single-cell data
scdiffeq
scDiffEq: modeling single-cell dynamics using neural differential equations.
adata-query
Fetch and format data matrices from AnnData
scdiffeq-analyses
Notebooks, figures, files, and helper functions to reproduce the analyses presented in the scDiffEq manuscript.
LARRY-dataset
LARRY Dataset: lineage and RNA recovery
cell-data
Cell data
torch-adata
torch-adata: bridging AnnData-based data models to torch.
ABCParse
A better base class to automatically parse local args.
neural-diffeqs
Neural differential equations made easy.
torch-nets
API to compose PyTorch neural networks on the fly.
parallel-execution
parallel execution in python; multithreading
perturb-tools
perturb-tools - Analysis Framework for Pooled CRISPR Genome Editing Screens.
py-pkg-logging
Python Package Logging Assistant.
ezpyplot
Python plotting assistant.
color-wizard
Color palette wizard.
cell-perturb
Impart in silico perturbations to observed cell states in AnnData.
cellplots
Cell-based data- & genomics-forward plotting assistant.
autodevice
Automatically assign available hardware on the fly, in-line with PyTorch code.
torch-pba
PyTorch implementation of PBA.
cell-ann
cell-ann: Cell approximate nearest neighbors
cell-voyager
Voyager for cell data.
cell-embeddings
Cell embeddings
cell-transformer
API for interfacing transformers with singel-cell data.
cell-cloud
Cloud-API for Cell Storage
quintessence-cell-engine
Engine
dgex
dgex
scdiffeq-plots
Plotting functions associated wtih analyses from scDiffEq
calicode
calicode
playmaker
Generative models of NFL player gametime action.
vinplots
vinplots - plotting assistant
brownian-diffuser
Brownian diffuser
cell-dynamics
Cell dynamics library.
mev-thesis
Michael E. Vinyard's PhD Thesis
michaels-thesis
Michael Vinyard's PhD Thesis
quintessential-hematopoiesis
The essence of hematopoiesis.
quintessence
The essence of a biological process.
hematopoiesis
The essence of hematopoiesis.
annoyance
annoyance - single-cell AnnData wrapper of Spotify's Annoy library.
torch-composer
API to compose pytorch neural networks
lightning-tutorial
pytorch-lightning tutorial
WebFiles
Download and read files from the web.
pydk
Python Developer Kit
flexinet
Flexible torch neural network architecture API
catnip-bio
catnip
lightning-diffeqs
PyTorch Lightning DiffEqs
ArchR-h5ad
ArchR_h5ad: Read .arrow files (from ArchR) to anndata.
GTFast
GTFast - cache and subset a `.gtf` file as a `.csv` for faster subsequent use.
licorice-font
licorice - vibrant string color additions.
cell-fate
cell_fate - models and benchmarking. Not exhuastive.
cell-command
Cell Command - Intergalactic force commanding Cell Rangers.
anngtf
anngtf - lift annotations from a `.gtf` file to your AnnData object.
cell-tools
cell_tools - Analysis Tools for Single-Cell Data
ann-nmf
ann_nmf - AnnData wrapper of the ARD-NMF module from SignatureAnalyzer
anndata-sdk
anndata_sdk
cell-ai
cell-ai - vibrant models expressive of cell states
ann-gsea
ann-gsea - integrate GSEA molecular signatures with AnnData
clonnotate
clonnotate
clone-data
clone-data
ancestry
ancestry
pool-sharq
pool-sharq: python interface for Broad Institute GPP's poolq software.
pyrequisites
pyrequisites
chopyn
chopyn
beethoven
beethoven
genomeIO
genomeIO
sglib
--
cell-library
--
simple-cell
simple-cell
hugging-cell
hugging-cell
guideID
guideID. A vintools package.
pythonome
pythonome - a python framework for functional genomics analysis workflows.
pythonomics
pythonomics - a python framework for functional genomics analysis workflows.
pyome
pyome - a python framework for functional genomics analysis workflows.
seq-toolkit
seq-toolkit - Basic sequence manipulation tools. A vintools package.
find-my-pam
find_my_pam. A vintools package.
pytrellis
pytrellis
cellkit
cellkit
pyrequisite
pyrequisite
nuts-and-bolts
nuts-and-bolts
chardonnay
chardonnay - vibrant color additions.
fauvism
fauvism - vibrant color additions.
vintner
vintner
brut
brut
bordeaux
bordeaux
vitaceae
vitaceae
vitis
vitis
PRESCIENT.nb
PRESCIENT.nb - a notebook-based, interactive implementation of PRESCIENT.
PRESCIENTnb
PRESCIENT.nb - a notebook-based, interactive implementation of PRESCIENT.
data-barrel
data-barrel - Data storage and loading API. A vintools package.
pyLaCroix
pyLaCroix - a python color palette for those that love sparkling water.
crispr-screen
crispr_tools - Analysis Tools for CRISPR Screen Design and Analysis
screen-tools
crispr_tools - Analysis Tools for CRISPR Screen Design and Analysis
crispr-tools
crispr_tools - Analysis Tools for CRISPR Screen Design and Analysis
vintools
vintools - Michael Vinyard's utilities.
sc-tools
sc-tools - Analysis Tools for Single-Cell Data
sc-catnip
sc-catnip - single-cell chromatin accessibility analysis tools in python
sc-utils
sc-utils: utility functions for single-cell analysis.
picrust
Holds the pi together.
nodescape
nodescape package
arancini
scATAC-seq utils
