umap package Search Results


umap  (RStudio)
90
RStudio umap
Umap, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/umap/product/RStudio
Average 90 stars, based on 1 article reviews
umap - by Bioz Stars, 2026-06
90/100 stars
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umap package  (InterStudy Inc)
90
InterStudy Inc umap package
Data pre-processing and batch correction. ( a ) Boxplots showing global array expression distribution in GSE9348 before (top) and after (bottom) normalization using frozen Robust Multiarray Averaging (fRMA). ( b ) <t>UMAP</t> plots showing successful identification (left) and removal (right) of inter-study batch effects with preservation of normal, adenoma, and colon cancer biological signatures (bottom) through empirical Bayes estimation method (ComBat). ( c ) Confusion table comparing the co-clustering of each known sample type (rows) with their predicted clusters (columns) based on 1,000 bootstraps of the density-based UMAP algorithm. Both the number of samples and their percentage of total are provided. ( d ) Boxplot comparing the distribution of array variances between the batch uncorrected (fRMA only) and batch corrected (fRMA + ComBat) Meta-datasets. Statistical significance was determined using a Wilcoxon signed-rank test.
Umap Package, supplied by InterStudy Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/umap package/product/InterStudy Inc
Average 90 stars, based on 1 article reviews
umap package - by Bioz Stars, 2026-06
90/100 stars
  Buy from Supplier
umap r package  (KNIME GmbH)
90
KNIME GmbH umap r package
Data pre-processing and batch correction. ( a ) Boxplots showing global array expression distribution in GSE9348 before (top) and after (bottom) normalization using frozen Robust Multiarray Averaging (fRMA). ( b ) <t>UMAP</t> plots showing successful identification (left) and removal (right) of inter-study batch effects with preservation of normal, adenoma, and colon cancer biological signatures (bottom) through empirical Bayes estimation method (ComBat). ( c ) Confusion table comparing the co-clustering of each known sample type (rows) with their predicted clusters (columns) based on 1,000 bootstraps of the density-based UMAP algorithm. Both the number of samples and their percentage of total are provided. ( d ) Boxplot comparing the distribution of array variances between the batch uncorrected (fRMA only) and batch corrected (fRMA + ComBat) Meta-datasets. Statistical significance was determined using a Wilcoxon signed-rank test.
Umap R Package, supplied by KNIME GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/umap r package/product/KNIME GmbH
Average 90 stars, based on 1 article reviews
umap r package - by Bioz Stars, 2026-06
90/100 stars
  Buy from Supplier

Image Search Results


Data pre-processing and batch correction. ( a ) Boxplots showing global array expression distribution in GSE9348 before (top) and after (bottom) normalization using frozen Robust Multiarray Averaging (fRMA). ( b ) UMAP plots showing successful identification (left) and removal (right) of inter-study batch effects with preservation of normal, adenoma, and colon cancer biological signatures (bottom) through empirical Bayes estimation method (ComBat). ( c ) Confusion table comparing the co-clustering of each known sample type (rows) with their predicted clusters (columns) based on 1,000 bootstraps of the density-based UMAP algorithm. Both the number of samples and their percentage of total are provided. ( d ) Boxplot comparing the distribution of array variances between the batch uncorrected (fRMA only) and batch corrected (fRMA + ComBat) Meta-datasets. Statistical significance was determined using a Wilcoxon signed-rank test.

Journal: Scientific Data

Article Title: A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression

doi: 10.1038/s41597-021-00998-5

Figure Lengend Snippet: Data pre-processing and batch correction. ( a ) Boxplots showing global array expression distribution in GSE9348 before (top) and after (bottom) normalization using frozen Robust Multiarray Averaging (fRMA). ( b ) UMAP plots showing successful identification (left) and removal (right) of inter-study batch effects with preservation of normal, adenoma, and colon cancer biological signatures (bottom) through empirical Bayes estimation method (ComBat). ( c ) Confusion table comparing the co-clustering of each known sample type (rows) with their predicted clusters (columns) based on 1,000 bootstraps of the density-based UMAP algorithm. Both the number of samples and their percentage of total are provided. ( d ) Boxplot comparing the distribution of array variances between the batch uncorrected (fRMA only) and batch corrected (fRMA + ComBat) Meta-datasets. Statistical significance was determined using a Wilcoxon signed-rank test.

Article Snippet: Following fRMA normalization, arrays from individual datasets were merged by matching probe.s Interstudy batch effects were identified by Uniform Manifold Approximation and Projection (UMAP) using the umap (version 0.2.7.0) package and removed using the original parametric iteration of ComBat within the sva (version 3.38.0) package .

Techniques: Expressing, Preserving