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umap
Here are 94 public repositories matching this topic...
An R package implementing the UMAP dimensionality reduction method.
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Jun 5, 2021 - R
JavaScript implementation of UMAP
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Oct 14, 2020 - JavaScript
Manage map and features with Leaflet and expose them for backend storage through an API.
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Feb 3, 2018 - JavaScript
Parametric UMAP embeddings for representation and semisupervised learning. From the paper "Parametric UMAP: learning embeddings with deep neural networks for representation and semi-supervised learning" (Sainburg, McInnes, Gentner, 2020).
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Feb 8, 2021 - Jupyter Notebook
Uniform Manifold Approximation and Projection - R package
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Dec 10, 2020 - R
Uniform Manifold Approximation and Projection (UMAP) implementation in Julia
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May 26, 2021 - Julia
Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
clustering
dropout
batch-normalization
imputation
scrna-seq
diffusion-maps
clustering-algorithm
3d
umap
normalization
10xgenomics
cell-type-classification
intractive-graph
cite-seq
singel-cell-sequencing
pseudotime
scvdj-seq
icellr
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Jun 9, 2021 - R
This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
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May 21, 2021 - R
R package for dimensionality reduction of small datasets
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May 22, 2021 - R
Seurat meets tidyverse. The best of both worlds.
ggplot2
dplyr
tidyverse
pca
transcripts
single-cell
tsne
umap
normalization
tibble
tidyr
sct
purrr
single-cell-rna-seq
seurat
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Jul 22, 2021 - R
A JavaScript Library for Dimensionality Reduction
clustering
matrix
javascript-library
pca
dimensionality-reduction
t-sne
mds
unsupervised-learning
lle
umap
isomap
fastmap
ltsa
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Jul 16, 2021 - HTML
create "Karpathy's style" 2d images out of your image embeddings
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Mar 23, 2021 - Python
Comparing FC VAE / FCN VAE / PCA / UMAP on MNIST / FMNIST
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Jul 7, 2018 - Jupyter Notebook
Workshop (6 hours): Clustering (Hdbscan, LCA, Hopach), dimension reduction (UMAP, GLRM), and anomaly detection (isolation forests).
clustering
dimensionality-reduction
unsupervised-learning
umap
hdbscan
isolation-forests
glrm
latent-class-analysis
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Jun 8, 2020 - R
A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.
visualization
machine-learning
dimensionality-reduction
nearest-neighbors
single-cell
graph-layout
umap
diffusion-process
denoising
high-dimensional
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Apr 4, 2021 - Python
davisidarta
commented
May 6, 2021
Hi! This is fantastic work, congratulations!
I'm, however, saddened by the somewhat hard-coded kNN graph computation, based solely on PCA, which can be misleading if data does not necessarily lie in a series of linear subspaces. A huge deal of work has been done lately on dimensional reduction, and thus restricting the kNN graphs to PCA is an important limitation. Is there any way to compute th
Tera Online 64-bit client package(*.gpk, *.gmp, *.upk, *.umap, *.u) editor/viewer
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Jul 24, 2021 - C++
R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
python
wrapper
bioinformatics
dimensionality-reduction
tsne
forceatlas2
umap
dimension-reduction
force-directed-graphs
wrappers
seurat
singlecellexperiment
singlecellexperiment-objects
paga
phate
opentsne
pacmap
dimensional-reduction
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Mar 22, 2021 - R
BEER: Batch EffEct Remover for single-cell data
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May 10, 2021 - R
C# library for fast embeddings projection using Uniform Manifold Approximation and Projection
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Jun 16, 2021 - C#
A Uniform Manifold Approximation and Projection (UMAP) library for Java, developed by Tag.bio in collaboration with Real Time Genomics.
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Feb 23, 2021 - Java
An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization
tf-idf
louvain
umap
single-cell-rna-seq
single-cell-analysis
rcppparallel
phenograph
jaccard-coefficient
idetify-active-pathways
single-cell-clustering
gf-icf
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Jul 20, 2021 - C++
Progressive Uniform Manifold Approximation and Projection (EuroVis 2020, short paper)
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Jun 8, 2021 - C++
"uMap let you create maps with OpenStreetMap layers in a minute and embed them in your site."[uMap Website]
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May 14, 2020 - Shell
Using word embeddings, TFIDF and text-hashing to cluster and visualise text documents
clustering
dimensionality-reduction
text-processing
d3js
document-clustering
umap
computational-social-science
text-clustering
text-features
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Nov 7, 2019 - Python
deep learning and scientific computing library with native CPU and GPU backend for the Scala programming language
machine-learning
scala
deep-learning
gpu
neural-networks
scala-library
tensor
umap
libtorch
extratrees
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Jul 22, 2021 - Scala
represent each cell in UMAP plots as a pie chart
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Jun 21, 2021 - Python
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Following up on the discussion here, it would be good to document how to get reproducible results with UMAP.
I think we should consider changing
random_statein the UMAP constructor to a seed (e.g. 42, like the newtransform_seeddefault) so that UMAP is reproducible by default.We should document that users can set `ran