Showing : SingleCellExperiment • reset
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 5 days ago by ★ 4.2k • written 10 days ago by • 0
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
10 days ago • updated 9 days ago Stefano Mangiola ▴ 10
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4
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241
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
16 days ago • updated 15 days ago vohara4 • 0
4
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1
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510
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 5 months ago by 66k • written 5 months ago by ▴ 20
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6
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
5 months ago Dario Strbenac ★ 1.5k
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rpk per cell saved in SCE object.
SingleCellExperiment
5 months ago JalapenoCornbread • 0
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
6 months ago elgomez • 0
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3
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605
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Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 6 months ago by • 0 • written 6 months ago by • 0
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554
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 8 months ago by • 0
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5
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944
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
10 months ago duez.tolga • 0
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1.0k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
12 months ago Matvii Mykhailichenko • 0
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2
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942
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
12 months ago Lluís Revilla Sancho ▴ 730
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3
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2.2k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
14 months ago mollyab12 • 0
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1
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1.2k
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Rename colData column
SingleCellExperiment colData rename
updated 16 months ago by ▴ 780 • written 16 months ago by ▴ 10
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3
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1.7k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 17 months ago by ▴ 10 • written 5.4 years ago by ▴ 10
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3
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1.8k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
21 months ago merv ▴ 130
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2
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842
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
21 months ago k1m ▴ 20
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4
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990
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
21 months ago Romina • 0
1
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1
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1.2k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 22 months ago by ▴ 740 • written 22 months ago by ▴ 130
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1
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2.8k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
22 months ago merv ▴ 130
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
22 months ago merv ▴ 130
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3
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1.6k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 23 months ago by 66k • written 23 months ago by ▴ 10
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1.0k
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Use of Scater for QC in scRNA-seq: How to remove cells with less than certain number of genes supported with certain number of reads
SingleCellExperiment
updated 2.0 years ago by ★ 4.2k • written 2.0 years ago by • 0
2
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5
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4.4k
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Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 16 months ago by • 0 • written 2.2 years ago by ▴ 10
2
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1
reply
1.2k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
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2
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985
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.4 years ago • updated 2.3 years ago msn ▴ 10
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747
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.4 years ago by 66k • written 2.4 years ago by • 0
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2
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1.2k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.5 years ago by ★ 4.2k • written 2.5 years ago by ▴ 40
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667
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.6 years ago Núria • 0
1
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2
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887
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
2.6 years ago Fatima • 0
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3
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1.7k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.7 years ago enricoferrero ▴ 660
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2.8k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.9 years ago by ★ 4.2k • written 2.9 years ago by • 0
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5
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5.1k
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.1 years ago by ▴ 60 • written 3.2 years ago by ▴ 20
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3
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1.4k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.4 years ago by ▴ 160 • written 3.4 years ago by • 0
3
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2
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2.4k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.4 years ago camerond • 0
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7
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2.2k
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.4 years ago bge • 0
1
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3
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1.9k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 10
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5
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2.4k
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 660
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2
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1.3k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
3.5 years ago achaillon • 0
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3
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1.1k
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singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 3.5 years ago by ▴ 70 • written 3.5 years ago by • 0
2
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3
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1.6k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.5 years ago achaillon • 0
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2
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1.5k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.6 years ago • updated 3.5 years ago jirkanov • 0
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2
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2.1k
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Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.6 years ago lirongrossmann ▴ 50
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1
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868
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 50
2
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7
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2.8k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.6 years ago by ★ 28k • written 3.6 years ago by ▴ 40
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6
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2.7k
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 80
1
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1
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1.2k
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Biological replicates in single cell experiments DE
singleCellExperiment
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
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4
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1.4k
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marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 50
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0
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773
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Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.9 years ago lirongrossmann ▴ 80
0
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3
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2.1k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 50
50 results • Page 1 of 1
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Answer: Ranking the GSEA Results by Michael Love 42k
Some posts on this topic: https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR by Gordon Smyth 51k
edgeR allows observation specific offsets (as already pointed out), although I am not confident that would be a reliable solution to your p…
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
Thank you I will take a look at those !
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
I will send you an email and talk to my advisor about setting up a meeting. Thank you !
Comment: Research Project - Expanding search funtionality on the GEO database by Sean Davis 21k
You can use the Bioconductor Annotation packages for the Affymetrix chips of interest. - https://bioconductor.org/packages/release/BiocVie…
Votes
Answer: DESeq2 time course using fitted splines
Answer: DESeq2 time course using fitted splines
Comment: Difference between enrichGO results and Enrichr website results
Answer: Struggling to convert a large list of non-model genes into human orthologs, any
A: makeContrasts from limma overides "i" as a varible
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