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2
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2.8k
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updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
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Cannot Install WGCNA
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updated 3.6 years ago by 4.3k • written 3.6 years ago by • 0
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4
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Why Negative value from GSVA
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3.6 years ago • updated 3.5 years ago Yang Shi ▴ 10
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3
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Low Differentially Bound Sites found with DiffBind
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3.6 years ago • updated 3.5 years ago gannoncottone • 0
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0
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regulondb version fixed to 10.8?
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3.6 years ago a.giachino2 • 0
0
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1
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2.2k
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Diffbind analysis of ATAC-seq data
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updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
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3
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Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
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1
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1
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833
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how do singleton samples contribute to dispersion estimate in DESeq2?
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updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
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3
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Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
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updated 3.2 years ago by ▴ 60 • written 3.6 years ago by • 0
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Error message: Could not find function "DESeqDataSetFromMatrix"
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3.6 years ago • updated 3.5 years ago Md. Faridul • 0
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How to create consensus network from SampledBlockwiseModules in WGCNA?
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3.6 years ago as8020 • 0
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1
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fetaure counts err
featurecounts
updated 3.5 years ago by ★ 3.6k • written 3.6 years ago by • 0
0
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2
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1.5k
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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
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bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
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updated 3.6 years ago by ★ 1.6k • written 3.6 years ago by • 0
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ACMG Annotations for Variants in R
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3.6 years ago hamza_karakurt ▴ 60
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3
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Can't Install ensembldb and EnsDb.Hsapiens.v86
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3.6 years ago elmfinds • 0
0
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2
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1.3k
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Number of rows in DESeq2 output (.csv) is not the same as number of rows in the results(dds) dataframe
output difference
3.6 years ago Jamie • 0
0
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0
replies
1.1k
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News: Translation Hackathon (community event) announcement
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3.6 years ago kozo.nishida • 0
1
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6
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Error while running DESeq2
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3.6 years ago srikar • 0
1
vote
0
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1.0k
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Mapping patient dataset onto control dataset
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3.6 years ago hamiltond ▴ 10
0
votes
4
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1.7k
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rename phenotypic variables in pData (microarray) or colData (RNA-Seq)
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3.6 years ago • updated 3.5 years ago jogugil • 0
0
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1
reply
822
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Error
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updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
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8
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How to get DESeq2 results for a list of genes
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3.6 years ago Lucía ▴ 30
0
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0
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958
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nearest and nearestKNeighbors with k=1 produce different results
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3.6 years ago Simon Coetzee ▴ 50
2
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2
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ComplexHeatmap: Change font size of annotation axis values
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updated 2.5 years ago by • 0 • written 3.6 years ago by ▴ 10
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1
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setting sizeFactors from scran :: caculateSumFactors.
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updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
1
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2
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6.2k
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Unable to open hd5 file using rhdf5 but can list contents
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updated 3.6 years ago by ★ 6.6k • written 3.6 years ago by • 0
2
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3
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Combine GRanges(List) to a single GRanges with unified breakpoints
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3.6 years ago Rodrigo • 0
5
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5
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package 'BiocInstaller' is not available (for R version 3.4.4)
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updated 3.6 years ago by 68k • written 3.6 years ago by • 0
2
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6
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Limma beta coefficient confidence intervals
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3.6 years ago fluentin44 • 0
5
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8
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Confused about the CPM and TMM normalization in edgeR
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updated 17 months ago by ▴ 60 • written 3.6 years ago by ▴ 30
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4
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Alternative for wininet method in tximeta
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3.6 years ago uhlkatie • 0
0
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4
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how to get the gene set from online GO database
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3.6 years ago • updated 3.5 years ago pengmin.wang.1 • 0
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818
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coseq does not find object "cap"
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3.6 years ago JaneDoe • 0
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1
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Pick some clusters to run trajectory and pseudotime analysis on Monocle3
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updated 2.8 years ago by • 0 • written 3.6 years ago by ▴ 10
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Calculating tumour purity having only CNA data
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3.6 years ago JAcky • 0
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bootstrapNullAlternativeModel() returns error
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3.6 years ago Tobias ▴ 40
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During dba(sampleSheet = "samples.csv") step, Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=charac…
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updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
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Compare different cell lines with tissues using limma
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updated 3.6 years ago by 53k • written 3.6 years ago by • 0
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Error "DESeqDataSetFromMatrix" function not found
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updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
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Can´t install GenomicRanges and rtracklayer
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updated 3.6 years ago by 68k • written 3.6 years ago by • 0
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How fix lines of dendrogram that overlap in the column portion of a heatmap?
heat heatmaps
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
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set.seed in function vs clusterSetRNGStream: switching from one to another
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3.6 years ago ZheFrench ▴ 60
3
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2
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FeaturePlot in scater
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3.6 years ago Guandong Shang ▴ 40
0
votes
3
replies
2.4k
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How can i fix this problem in R
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updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
votes
1
reply
1.6k
views
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 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
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0
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1.5k
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
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3.6 years ago Palmira • 0
0
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2
replies
6.3k
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
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3.6 years ago Bhavana • 0
0
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1
reply
1.2k
views
What are the data values in qRT-PCR for statistical testing? dCT? or 2^-dCT?
qRT-PCR CTvalue
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
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updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
46,730 results • Page 84 of 935
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Replies
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
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Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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