3
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9
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3.5k
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Question about filter by expression (filterByExpr) in edgeR
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2.7 years ago mohammedtoufiq91 ▴ 10
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1.1k
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what does "exp1" mean in the gage() function?
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updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
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Access modalities in h5 files to extract expression and atac data from 10xh5
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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Multifactorial Design for DESEQ2
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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777
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How to adjust plots generated using psygenet2r?
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updated 2.7 years ago by ▴ 70 • written 2.7 years ago by ▴ 20
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Doubt about expression data as well as assay
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updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
3
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DESeq2 lfcShrink: swapping reference gives different results for the same comparison
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2.7 years ago Daphnia • 0
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2
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
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2.7 years ago Giulia • 0
2
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1
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4.2k
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DiffBind on ATAC seq data
ATACSeq
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 20
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3
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deseq2 normalization and statistical method
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
0
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0
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837
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
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2.7 years ago Giulia • 0
1
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2
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
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2.7 years ago garbuzov • 0
0
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0
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796
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Plot profiles for each group - spline analysis in edgeR
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updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 740
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Compare and filter three BAM files
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2.7 years ago wt215 • 0
1
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1
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993
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FlowSOM with unrelated channels
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updated 2.7 years ago by ▴ 70 • written 2.7 years ago by • 0
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2.7 years ago allanokwaro • 0
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1
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Specific versions of packages
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updated 2.7 years ago by ★ 6.6k • written 2.7 years ago by ▴ 90
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1
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Error in h5checktype(). H5Identifier not valid.
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updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
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13
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KEGG enrichment in R and gene IDs
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2.7 years ago Laia ▴ 10
3
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1
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876
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How edgeR estimate the common dispersion?
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2.8 years ago • updated 2.7 years ago Dan • 0
0
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6
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1.2k
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DispEsts plot
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2.7 years ago Sep • 0
0
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0
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720
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getGEO error when trying to download a series matrix file
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2.7 years ago suyonj • 0
1
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3
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Correct script for featurecounts in Rsubread
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2.7 years ago rmoorehe • 0
0
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1
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791
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Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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Align to reference genome
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
4
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4
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Can I run DESeq2 with SMART-Seq data
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2.7 years ago Assa Yeroslaviz ★ 1.5k
0
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How to change the dot size in plotPCA?
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updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
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5
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[limma::kegga] Pathway names all NA
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written 2.7 years ago by • 0
0
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1
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972
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How to extract proteins from PCs in plot_pca in DEP package
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updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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3
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How to getting synonymous SNPs from BiomaRt before timing out?
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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News: Bioconductor 3.17 db0s, OrgDbs, and TxDbs now available
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2.7 years ago kayla.interdonato ▴ 160
2
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807
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Are polynomial contrasts for a time factor possible in DESeq2?
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
1
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7
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MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
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updated 2.7 years ago by • 0 • written 4.7 years ago by • 0
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801
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deseq2 nested multifactorial analysis
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updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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2.7 years ago edward.esiribloom • 0
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Limma for Fluidigm high throughput PCR
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updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
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How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
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updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
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5.5k
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does anyone how to create rarefaction curves from a phyloseq object?
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updated 2.7 years ago by ▴ 20 • written 2.7 years ago by • 0
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Human to mouse SNP conversion
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2.7 years ago bonheur • 0
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2
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Help understanding dispersion values and why so many genes change significance after removing low read samples
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2.7 years ago Miriam • 0
6
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6
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minfi support of illumina Infinium methylationEPIC v2.0
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updated 14 months ago by • 0 • written 2.7 years ago by ▴ 50
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Time-course, comparison of two groups
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2.7 years ago boczniak767 ▴ 740
0
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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Job: Postdoc at EMBL: spatial and single-cell computational biology for precision oncology, based in Heidelberg, Germany
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2.7 years ago Wolfgang Huber ★ 13k
1
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3
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How to compute(calculate) rlog and vst provided from DESeq2
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2.7 years ago tstpp • 0
0
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1
reply
773
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Outlier removal outcome
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updated 2.7 years ago by ★ 5.0k • written 2.8 years ago by • 0
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8
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TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
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2.7 years ago davidhillis • 0
2
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7
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limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 40
1
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2
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757
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DESeq2 pvalues overly conservative
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2.7 years ago gdolsten ▴ 10
46,691 results • Page 57 of 934
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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BTW, I tested with no issue on MacOS ARM on our previous github issue.
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The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
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For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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