Showing : SC3 • reset
0
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3
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3.3k
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Installing SC3: gfortran error on Mac M1
SC3
3.6 years ago krp • 0
1
vote
4
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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
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7
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2.8k
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differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.8 years ago Bogdan ▴ 670
4
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5
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2.3k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.1 years ago by ▴ 150 • written 6.1 years ago by ▴ 60
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2
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1.3k
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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
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1
reply
1.6k
views
SC3 how to customize plots ?
SC3 plot consensus marker heatmap
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by • 0
0
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2
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1.1k
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Failure to cluster SC3
SC3
updated 6.5 years ago by ▴ 150 • written 6.6 years ago by • 0
1
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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
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2
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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
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1
reply
1.1k
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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
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1
reply
1.5k
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SC3 Package: marker genes and normal genes obtained from featureData
SC3
updated 7.3 years ago by ▴ 150 • written 7.4 years ago by • 0
1
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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
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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 8.0 years ago by ▴ 150 • written 8.0 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
2.3k
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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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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