2
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4
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1.5k
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limma with or without intercept gives different results
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2.7 years ago Sydney • 0
3
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9
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Question about filter by expression (filterByExpr) in edgeR
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2.7 years ago mohammedtoufiq91 ▴ 10
0
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1
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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
0
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1
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1.6k
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
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2
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1.3k
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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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1
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778
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How to adjust plots generated using psygenet2r?
psygenet2r
updated 2.7 years ago by ▴ 70 • written 2.7 years ago by ▴ 20
0
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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
0
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2
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2.1k
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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
views
DiffBind on ATAC seq data
ATACSeq
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 20
2
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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?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
1
vote
2
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1.8k
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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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798
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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
0
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2
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1.2k
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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
reply
996
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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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806
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Module Trait Corelation
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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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2.2k
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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
reply
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
replies
722
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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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793
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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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0
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646
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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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3
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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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2.3k
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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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973
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How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
0
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3
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How to getting synonymous SNPs from BiomaRt before timing out?
biomaRt SNP
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
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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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1
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808
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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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802
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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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cpgCollapse error
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2.7 years ago edward.esiribloom • 0
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4
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Unable to create venndiagram using VennDiagram 1.5.1 package
updated 2.7 years ago by • 0 • written 13.1 years ago by ▴ 10
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931
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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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4
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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
2
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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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0
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Human to mouse SNP conversion
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2.7 years ago bonheur • 0
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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20
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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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1
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2.2k
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DESeqDataSetFromMatrix NA values
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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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1.3k
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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
votes
1
reply
774
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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
votes
7
replies
1.7k
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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
46,692 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()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
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…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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