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Package Usage: pypi: graphtools

graphtools
25 versions
Latest release: over 1 year ago
12 dependent packages
4,415 downloads last month

View more package details: https://packages.ecosyste.ms/registries/pypi.org/packages/graphtools

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/KrishnaswamyLab%2Fgraphtools

Dependent Repos 27

KrishnaswamyLab/Multiscale_PHATE
Creating multi-resolution embeddings and clusters from high dimensional data
  • * requirements.txt
  • * setup.py

Size: 5.95 MB - Last synced: 2 months ago - Pushed: over 1 year ago

KrishnaswamyLab/MELD
Quantifying experimental perturbations at single cell resolution
  • >=0.1.8.1 doc/source/requirements.txt
  • >=1.5.0 requirements.txt
  • >=1.5.0 setup.py

Size: 17.9 MB - Last synced: 3 days ago - Pushed: 10 months ago

pwwang/immunopipe
Integrative analysis for scTCR- and scRNA-seq data
  • ==1.5.2 docker/environment.yml

Size: 19.4 MB - Last synced: 6 days ago - Pushed: 7 days ago

stanleyjs/SR3
SR3 Fusion Clustering for multimodal data
  • * setup.py

Size: 7.55 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago

linz94/birdcatdetection
  • ==1.5.2 requirements.txt

Size: 10.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

burtonrj/CytoTools
Tools and utilities for analysing cytometry data in Python
  • 1.5.2 poetry.lock

Size: 19.4 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

xuesoso/singleToxoplasmaSeq 📦
A respository that includes scripts and jupyter notebooks to re-generate analysis results of "A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression" (2020).
  • ==0.1.9 requirements.txt

Size: 5.9 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

KrishnaswamyLab/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
  • >=1.3.1 Python/requirements.txt
  • >=1.3.1 Python/setup.py

Size: 142 MB - Last synced: about 1 month ago - Pushed: 3 months ago

KrishnaswamyLab/MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
  • >=1.0.0 python/doc/source/requirements.txt
  • >=1.4.0 python/requirements.txt
  • >=1.4.0 python/setup.py

Size: 216 MB - Last synced: 11 days ago - Pushed: over 1 year ago

dnordfors/archetypes
Occupational Archetypes - a 'Myers Briggs for jobs'
  • ==1.1.0 workspace/pip_requirements.txt

Size: 218 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

hernet/SingleFlow
SingleFlow is a pipeline for analyzing scRNA-seq data.
  • ==0.1.10 requirements.txt

Size: 48.8 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

scottgigante/m-phate
Multislice PHATE for tensor embeddings
  • >=1.1 doc/source/requirements.txt

Size: 135 MB - Last synced: 4 days ago - Pushed: about 3 years ago

JoshuaHess12/miaaim-python
MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds
  • ==1.5.1 notebooks/hdiprep/001-1-requirements.txt
  • ==1.5.1 notebooks/hdiprep/001-requirements.txt
  • ==1.5.1 notebooks/hdireg/001-2-requirements.txt
  • ==1.5.1 notebooks/patchmap/001-3-requirements.txt

Size: 20.9 MB - Last synced: 19 days ago - Pushed: over 2 years ago

arguz95/Project_ML2
This is the final project for INSY695 - Enterprise Data Science and ML in Production II - Arnaud, Jules, Ram, Dorothy and Rameez
  • ==1.5.2 requirements.txt

Size: 39 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

charbj/wiggle
Graphical user interface to integrate cryoEM flexibility analyses with ChimeraX
  • ==1.5.2 requirements.txt

Size: 1.48 MB - Last synced: 4 months ago - Pushed: 11 months ago

nijibabulu/metazoan_synteny
Ancient animal genome architecture reflects cell type identities
  • ==1.0.0 imputation/Pipfile.lock

Size: 81.1 KB - Last synced: 12 months ago - Pushed: almost 5 years ago

burtonrj/CytoPlots
A small package of plotting utilities for use when analysing cytometry data in Python
  • 1.5.2 poetry.lock

Size: 91.8 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

KrishnaswamyLab/DiffusionEMD
Code corresponding to the paper Diffusion Earth Mover's Distance and Distribution Embeddings
  • * requirements.txt
  • * setup.py

Size: 532 KB - Last synced: 11 days ago - Pushed: over 2 years ago

atong01/MultiscaleEMD
Multiscale earth mover's distance methods for tree and manifold structured data
  • * requirements.txt
  • * setup.py

Size: 7.03 MB - Last synced: 12 days ago - Pushed: 11 months ago

cscarv/riemannian-metric-learning-ot
  • ==1.5.2 requirements.txt

Size: 62.2 MB - Last synced: 11 months ago - Pushed: 11 months ago

aidos-lab/TARDIS
TARDIS: Topological Algorithms for Robust DIscovery of Singularities
  • 1.5.2 poetry.lock

Size: 6.44 MB - Last synced: 14 days ago - Pushed: 10 months ago

DataONEorg/d1_python
Python components for DataONE clients and servers
  • ==1.5.2 requirements.txt

Size: 90.3 MB - Last synced: 6 days ago - Pushed: 19 days ago

vishalbelsare/PHATE Fork of KrishnaswamyLab/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
  • >=1.3.1 Python/requirements.txt
  • >=1.3.1 Python/setup.py

Size: 134 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

laueste/algorithms-ucsf-2019
BMI 203, Winter 2019 at UCSF
  • ==1.0.0 hw2/requirements.txt

Size: 8.84 MB - Last synced: about 1 year ago - Pushed: about 5 years ago

KevinMoonLab/GRAE
Geometry Regularized Autoencoders (GRAE) for large-scale visualization and manifold learning
  • ==1.5.2 requirements.txt

Size: 22.8 MB - Last synced: 5 months ago - Pushed: 5 months ago

007gzs/test
  • * requirements.txt

Size: 1.6 MB - Last synced: 5 months ago - Pushed: 5 months ago

dapingtai/SingleCell
Single Cell Analysis Method
  • >=1.0.0 ExpressionRecoveryMaterials/MAGIC/python/doc/source/requirements.txt
  • >=1.4.0 ExpressionRecoveryMaterials/MAGIC/python/requirements.txt
  • >=1.4.0 ExpressionRecoveryMaterials/MAGIC/python/setup.py

Size: 32.9 MB - Last synced: about 1 year ago - Pushed: about 4 years ago

mnology/dotfiles
  • ==1.5.2 requirements.txt

Size: 76.2 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

rgs2151/HPML_Loss_Investigations
  • ==1.5.3 requirements_new.txt

Size: 122 MB - Last synced: 10 months ago - Pushed: about 1 year ago

KrishnaswamyLab/h_phate_demo
Demonstration of Hierarchical PHATE
  • * requirements.txt
  • * setup.py

Size: 27.3 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

KrishnaswamyLab/CATCH
Learning cellular hierarchy from scRNAseq data
  • * requirements.txt
  • * setup.py

Size: 39.5 MB - Last synced: 10 months ago - Pushed: over 2 years ago

KrishnaswamyLab/spARC
Denoising spatial transcriptomics data
  • ==1.5.2 requirements.txt
  • * setup.py

Size: 47.3 MB - Last synced: 3 months ago - Pushed: 8 months ago

makotu1208/open-problems-multimodal-3rd-solution
open-problems-multimodal-3rd-solution
  • ==1.5.2 requirements.txt

Size: 261 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

makotu1208/Otto-kaggle-solution-makotupart
kaggle:otto competition
  • ==1.5.2 requirements.txt

Size: 57.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

AstraZeneca/NESS
Official implementation of "NESS: Node Embeddings from Static Subgraphs"
  • ==1.5.3 requirements.txt

Size: 762 KB - Last synced: 5 months ago - Pushed: 12 months ago

metric-space-ai/phate
A Dimensionality Reduction Method for Visualizing Trajectory Structures in High-Dimensional Biological Data
  • * setup.py

Size: 34.2 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

NicholasCowie/Nicholas_Cowie_Masters_Thesis
This repository stores the data and scripts used to generate the results to this thesis
  • ==1.5.1 Models/Pipfile.lock

Size: 21.8 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago

ai408/omicverse Fork of Starlitnightly/omicverse
A python library for multi omics included bulk and single cell RNA-seq analysis.
  • >=1.5 pyproject.toml
  • * requirements.txt

Size: 397 MB - Last synced: 10 months ago - Pushed: 11 months ago

CodeYu001/lisflood-utilities Fork of ec-jrc/lisflood-utilities
LISFLOOD OS - Utilities
  • ==1.4.1 environment.yml

Size: 4.59 MB - Last synced: about 2 months ago - Pushed: over 3 years ago

tauhidstanford/PHATE Fork of KrishnaswamyLab/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
  • >=1.3.1 Python/requirements.txt
  • >=1.3.1 Python/setup.py

Size: 134 MB - Last synced: 10 months ago - Pushed: over 4 years ago

jakerhodes/RF-PHATE
Official RF-PHATE repository.
  • ==1.5.3 requirements.txt

Size: 3.45 MB - Last synced: 5 months ago - Pushed: 5 months ago

Bolin-BGI/Pyomic Fork of Starlitnightly/omicverse
A python framework library for multi omics included bulk and single cell analysis with Python.
  • * Pyomic.egg-info/requires.txt
  • * requirements.txt
  • * setup.py

Size: 271 MB - Last synced: 10 months ago - Pushed: about 1 year ago

lifanchen-simm/PHATE Fork of KrishnaswamyLab/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
  • >=1.3.1 Python/requirements.txt
  • >=1.3.1 Python/setup.py

Size: 141 MB - Last synced: 5 months ago - Pushed: 5 months ago

Starlitnightly/omicverse
A python library for multi omics included bulk and single cell RNA-seq analysis.
  • >=1.5 pyproject.toml

Size: 604 MB - Last synced: 5 months ago - Pushed: 6 months ago

samjleone/Graph-Fourier-MMD
  • * requirements.txt
  • * setup.py

Size: 6.86 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

Wu-Lab/SCARP_biorxiv
  • ==1.5.2 requirements.txt

Size: 3.61 MB - Last synced: 15 days ago - Pushed: over 1 year ago

NuttidaLab/NeuralEmbedder
Improving PHATE with Temporal AutoEncoders
  • >=1.5.3, requirements.txt
  • >=1.5.3 setup.py

Size: 10.1 MB - Last synced: 10 months ago - Pushed: about 1 year ago

hai178912522/omicverse Fork of Starlitnightly/omicverse
A python library for multi omics included bulk and single cell RNA-seq analysis.
  • >=1.5 pyproject.toml
  • * requirements.txt

Size: 132 MB - Last synced: about 1 month ago - Pushed: 9 months ago

ZhonghouXu/lisflood-code Fork of ec-jrc/lisflood-code
Lisflood OS - LISFLOOD
  • ==1.4.1 environment.yml
  • ==1.4.1 requirements.txt

Size: 922 MB - Last synced: 9 months ago - Pushed: over 2 years ago

yasark/Otto-kaggle-solution-makotupart Fork of makotu1208/Otto-kaggle-solution-makotupart
kaggle:otto competition 3rd place
  • ==1.5.2 requirements.txt

Size: 57.6 KB - Last synced: about 1 month ago - Pushed: over 1 year ago

NuttidaLab/NeuralDecoder
RSA techniques to interpret + quantify representations
  • ==1.5.3 requirements_doc.txt

Size: 10 MB - Last synced: 8 months ago - Pushed: 8 months ago

mandixbw/Cytophenograph Fork of luglilab/Cytophenograph
Pipeline for flow cytometry anlaysis
  • ==1.5.3 requirements.txt

Size: 363 MB - Last synced: about 1 month ago - Pushed: 9 months ago

DBinary/DouLabRotation_2023
This repository was used to contain the tutorials of telemere length calculation for single cell DNA-seq data.
  • * requirements.txt

Size: 3.43 MB - Last synced: 8 months ago - Pushed: 8 months ago

taoshengxu/MAGIC Fork of KrishnaswamyLab/MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
  • >=1.0.0 python/doc/source/requirements.txt
  • >=1.0.0 python/requirements.txt
  • >=1.0.0 python/setup.py

Size: 208 MB - Last synced: 8 months ago - Pushed: about 5 years ago

HungryAmoeba/hypergraph_scattering
Hypergraph scattering
  • 1.5.3 poetry.lock

Size: 60.9 MB - Last synced: 3 months ago - Pushed: 3 months ago

PabS729/small_LL_claim_classification
  • ==1.5.3 wandb/offline-run-20231106_195949-7k61au5k/files/requirements.txt

Size: 1.07 MB - Last synced: 7 months ago - Pushed: 7 months ago

Ambistic/FastCorr
  • ==1.5.2 requirements.txt

Size: 5.86 KB - Last synced: 8 months ago - Pushed: over 3 years ago

sibasmarak/CausalInferenceProject
  • ==1.5.3 requirements.txt

Size: 1.98 MB - Last synced: 6 months ago - Pushed: 6 months ago

noatgnu/cauldron
  • ==1.5.3 app/requirements.txt

Size: 24.7 MB - Last synced: 6 days ago - Pushed: 6 days ago

brickmanlab/riveiro-et-al-2023
  • ==1.5.3 environment.yml

Size: 31.8 MB - Last synced: 6 months ago - Pushed: 6 months ago

mccorsi/M2_CNN_Networks_BCI
  • ==1.5.2 requirements.txt

Size: 2.34 MB - Last synced: 6 months ago - Pushed: 7 months ago

ankitbha/dfdl_imputation
  • >=1.0.0 MAGIC/doc/source/requirements.txt
  • >=1.4.0 MAGIC/requirements.txt
  • >=1.4.0 MAGIC/setup.py

Size: 1.09 GB - Last synced: 3 days ago - Pushed: 3 days ago

AstraZeneca/SelfPAD
The official implementation of "Improving Antibody Humanness Prediction using Patent Data".
  • ==1.5.3 Pipfile
  • ==1.5.3 requirements.txt

Size: 425 KB - Last synced: 3 months ago - Pushed: 3 months ago

SergueiMoscow/s_media_deploy
  • ==1.5.3 requirements.txt

Size: 11.7 KB - Last synced: 4 months ago - Pushed: 4 months ago

anshika0911/kaizntree-backend-test
  • ==1.5.3 requirements.txt

Size: 43 KB - Last synced: 3 months ago - Pushed: 3 months ago

FarzamTP/BioNet
  • ==1.5.3 requirements.txt

Size: 116 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

brickmanlab/proks-salehin-et-al
Deep Learning Based Models for Preimplantation Mouse and Human Development
  • ==1.5.3 requirements.txt

Size: 69.2 MB - Last synced: 15 days ago - Pushed: 15 days ago

KrishnaswamyLab/TPHATE
  • * requirements.txt
  • >=1.5.3 setup.py

Size: 21.6 MB - Last synced: about 2 months ago - Pushed: 3 months ago