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Packages don't update, but no error or warning is thrown
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3 months ago gernophil • 0
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How to properly average normalized counts of biological replicates
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error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
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WGCNA coupled with differential expression analysis: question about baseline module detection
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
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overlapsAny for elements in GRangesList
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Which input file is used for DGEList in EgdeR?
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Adding a group of samples reduces DEGs in other groups
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biomaRt has encountered an unknown server error.
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updated 3 months ago by • 0 • written 3 months ago by • 0
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ComBat_seq function in sva package does not return a matrix
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News: Bioconductor 3.18 is Released!
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Archive location for Bioconductor packages
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
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limma output for epic array methylation data
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9 months ago Jitendra ▴ 10
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threshold to filter lowly expressed genes
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DataFrame Construction With Non-standard Column
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Differential protein/biomarker expression using limma: is that possible?
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updated 3 months ago by • 0 • written 3.2 years ago by ▴ 10
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DEG Filtering
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Problem about picking soft threshold power in WGCNA software
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Support for new Illumina human methylation EPIC array v2
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outdated GEOmetadb.sqlite
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Can the limma package be applied to Log2 RUV-normalized data?
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updated 5 months ago by • 0 • written 12 months ago by ▴ 10
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different number of DEG because of outliers
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limma: More differentially expressed genes when factor included in model than when used as blocking factor
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create COMPOUND dataset (2 matrices) with rhdf5?
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3 months ago baptiste ▴ 20
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 15 days ago by 65k • written 2.3 years ago by • 0
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Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
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6 months ago • updated 5 months ago kjngo ▴ 40
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Confusion about LFC using contrasts weights in EdgeR
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can't install DESeq2 ("unable to access index for repository")
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9 months ago Alessia ▴ 40
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Install DESeq2 problem for macbook pro M1 Max
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ASpli checks fail on Linux due to missing dependency to statmod
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Question about setting threshold using filtering by expression on genes in edgeR
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updated 11 months ago by 50k • written 11 months ago by ▴ 10
5
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PhD student
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10 months ago Nisha • 0
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19
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DiffBind GreyListChIP error: Error: BiocParallel errors
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updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
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6
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Monotonic genes in results of differential gene expression analysis
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3 months ago Shaimaa Gamal • 0
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
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3
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Log-cpm values from limma
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updated 7 days ago by 50k • written 29 days ago by • 0
4
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7
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should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
4
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4
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Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
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updated 9 weeks ago by • 0 • written 13 months ago by ▴ 10
1,738 results • Page 2 of 35
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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