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2
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265
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Regressing out batch effects
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updated 5 weeks ago by 42k • written 6 weeks ago by • 0
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188
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DESeq2 - Missing values in count matrix
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updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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DMRcate error need at least two non-NA values to interpolate
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6 weeks ago Macsue • 0
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CombineArrays for EPIC and EPIC V2
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6 weeks ago • updated 14 days ago Kim • 0
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updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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4
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
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updated 6 weeks ago by 50k • written 6 weeks ago by • 0
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edgeR analysis: glm functions and offset matrix
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6 weeks ago Marianna ▴ 20
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2
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
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6 weeks ago Gimena • 0
0
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6
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unable to access Annotationhub latest record
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Obtaining pheno data from CEL files
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6 weeks ago • updated 5 weeks ago Kurtis • 0
1
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1
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172
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DESeq2 , filter and theta arguments in resutlts()
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6 weeks ago Layal • 0
0
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2
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183
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pca with VST of DESeq2 give 100% variance in PC1
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6 weeks ago michelafrancesconi8 • 0
0
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1
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164
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Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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4
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286
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Abnormal Low Dispersion Gene Population in DESeq2
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updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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1
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123
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Brachypodium distachyon db
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updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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4
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447
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
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6 weeks ago Lucy ▴ 60
0
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2
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6 weeks ago Seongsu • 0
0
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174
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No output from read.bismark with bismark cov.files
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updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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2
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192
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Gene Ontology doubt
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6 weeks ago Bhawna • 0
0
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2
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314
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
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6 weeks ago fer_talavera • 0
1
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2
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MethylKit read issue
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updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
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2
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281
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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6 weeks ago • updated 28 days ago isaac.vock • 0
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7
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435
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Internet connection for Bioconductor packages in Rstudio in Iran...
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6 weeks ago needNGS • 0
0
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1
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190
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Convert transcriptomic bam to genomic bam?
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15
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23
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The difference when using Limma compare between 3 conditions vs 2 conditions
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7 weeks ago • updated 17 days ago Chris ▴ 10
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4
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Minfi - estimatecellscount
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updated 18 days ago by 65k • written 7 weeks ago by • 0
0
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0
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124
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
7 weeks ago feather-W • 0
0
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0
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120
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PCA plot for normalized counts using Diffbind
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7 weeks ago Ankit ▴ 20
1
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5
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364
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fgsea fork
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3
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Differing results from plotMDS and PCAtools
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updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
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6
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Doing comparison of RNA-seq data using EdgeR
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updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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175
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New genes that did not exist in dds object suddenly showed up after degPatterns
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updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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WGCNA: analysis of complex trait associations with regressions
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7 weeks ago • updated 6 weeks ago w.cookson • 0
0
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0
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109
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
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7 weeks ago Pierre Lindenbaum ▴ 10
0
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153
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Trimming a section of a scaffold from a genome
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updated 7 weeks ago by 65k • written 7 weeks ago by • 0
2
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3
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PCA of different bacterial species
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updated 7 weeks ago by 42k • written 7 weeks ago by ▴ 10
2
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8
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Microarray Limma Model fitting and DEG
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updated 7 weeks ago by 50k • written 7 weeks ago by • 0
1
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Problem with maplot {affy} method when using rma {affy} method output as its input
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7 weeks ago Mj.A. • 0
0
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2
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215
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
2
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256
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From a DNAStringSet to a data.frame
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7 weeks ago ramiro.barrantes ▴ 10
5
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25
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limma models out of memory issue on Slurm HPC
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0
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bioconductor emailing list
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updated 7 weeks ago by 3.9k • written 7 weeks ago by • 0
2
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3
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Rsubread crashes Rstudio while alignment
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updated 7 weeks ago by ★ 3.6k • written 7 weeks ago by • 0
3
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
7 weeks ago Anita ▴ 10
0
votes
0
replies
139
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
7 weeks ago gshweta95 • 0
2
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1
reply
252
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
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updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by ★ 1.5k
3
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3
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454
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Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
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updated 7 weeks ago by ▴ 160 • written 7 weeks ago by • 0
7
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6
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479
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Batch Effect Correction, Gene Filtering
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updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
2
replies
371
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The order of those tied genes will be arbitrary, which may produce unexpected results.
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8 weeks ago • updated 6 weeks ago Gordon • 0
2
votes
1
reply
230
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 7 weeks ago by ★ 4.0k • written 8 weeks ago by ▴ 10
45,667 results • Page 5 of 914
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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…
Votes
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
Rsubread counting peaks ATACseq
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