Showing : sc3 • reset
0
votes
3
replies
3.3k
views
Installing SC3: gfortran error on Mac M1
SC3
3.6 years ago krp • 0
1
vote
4
replies
2.0k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
0
votes
7
replies
2.8k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.8 years ago Bogdan ▴ 670
4
votes
5
replies
2.3k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.0 years ago by ▴ 150 • written 6.0 years ago by ▴ 60
0
votes
2
replies
1.3k
views
error running sc3_plot_de_genes in SC3 R package
SC3
updated 6.2 years ago by ▴ 150 • written 6.2 years ago by • 0
0
votes
1
reply
1.6k
views
SC3 how to customize plots ?
SC3 plot consensus marker heatmap
updated 6.3 years ago by ▴ 150 • written 6.4 years ago by • 0
0
votes
2
replies
1.1k
views
Failure to cluster SC3
SC3
updated 6.5 years ago by ▴ 150 • written 6.6 years ago by • 0
1
vote
1
reply
1.7k
views
A question about log_transformed
SC3
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
0
votes
2
replies
1.2k
views
How can I show certain gene's expression in clusters by sc3
sc3
updated 6.9 years ago by ▴ 150 • written 6.9 years ago by • 0
1
vote
1
reply
1.1k
views
Is there a way to pull out the stability index matrix from the SC3 object?
sc3
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ▴ 10
0
votes
1
reply
1.5k
views
SC3 Package: marker genes and normal genes obtained from featureData
SC3
updated 7.3 years ago by ▴ 150 • written 7.3 years ago by • 0
1
vote
1
reply
1.9k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.4 years ago by ▴ 150 • written 7.4 years ago by ▴ 10
1
vote
8
replies
2.9k
views
SC3_estimate_k formatting error?
sc3 scater
updated 7.4 years ago by ▴ 150 • written 7.4 years ago by ▴ 10
5
votes
2
replies
7.2k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment sc3 scater
updated 7.4 years ago by ▴ 150 • written 7.4 years ago by ▴ 10
4
votes
5
replies
2.3k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 20
1
vote
1
reply
1.7k
views
Does SC3 correct counts for gene length?
sc3 scater single-cell rna-seq biclustering
updated 7.6 years ago by ▴ 150 • written 7.7 years ago by ▴ 20
0
votes
1
reply
3.9k
views
Import .mtx file in R
sc3
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by • 0
4
votes
2
replies
1.7k
views
sc3_plot_expression, colour labels
sc3 single-cell
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by ▴ 20
3
votes
3
replies
1.6k
views
Sharing SC3_interactive results
SC3 single-cell shiny
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by ▴ 20
4
votes
3
replies
2.2k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by ★ 1.5k
2
votes
5
replies
2.2k
views
sc3_prepare function error
sc3 scater single-cell single cell
updated 8.2 years ago by ▴ 150 • written 8.2 years ago by ★ 1.5k
3
votes
2
replies
1.6k
views
SC3 tutorial error
SC3
updated 8.4 years ago by ▴ 150 • written 8.4 years ago by ▴ 30
3
votes
1
reply
1.6k
views
SC3 with latent variable corrected counts
SC3 single cell
updated 8.5 years ago by ▴ 150 • written 8.5 years ago by ▴ 10
23 results • Page 1 of 1
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Answer: edgeR::cpm() results in negative values from raw counts of 0 by ATpoint ★ 4.8k
The function, when `log = TRUE` adds a small prior count to the counts before taking the log, avoiding taking the log of 0. If that prior i…
Answer: edgeR::cpm() results in negative values from raw counts of 0 by James W. MacDonald 68k
It's calculated exactly how you might expect (it's called counts/million counts for a reason). ``` > y <- matrix(rnbinom(20,size=1,mu=…
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k
Thanks for posting this Kinnary. See also https://github.com/LieberInstitute/spatialLIBD/issues/106 for more details on the background.
Answer: Gene Ontology (GO) Analysis by James W. MacDonald 68k
The main difference is that `enrichGO` fits a conventional hypergeometric test whereas `hyperGTest` allows you to do a conditional test as …
Comment: blockwiseModule crashes in the end and doesn't generate modules by drivingdirectionsonline • 0
Solution: The error is likely due to a conflicting cor() function from another package (like psych). Restart R, run blockwiseModules() befo…
Votes
edgeR::cpm() results in negative values from raw counts of 0
Comment: Differential expression analysis using two TCGA datasets
C: Annotating HTA 2.0 genes
C: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
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