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DBT JRF & PhD Scholar
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8 hours ago Manisha • 0
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I am having issues with bowtie2_build
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updated 8 hours ago by 67k • written 1 day ago by • 0
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updated 9 hours ago by 43k • written 1 day ago by • 0
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0
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1 day ago cftattersfield • 0
1
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Events Community Training Africa Bioconductor
1 day ago Maria Doyle ▴ 100
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1
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How to visualize these pathways using pathview
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 2 days ago by ★ 1.4k • written 5 days ago by • 0
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3
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Job: Postdoc/RA position: Software Engineer For R and High-Performance Computing
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4
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674
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
4 days ago • updated 1 day ago Quang NN ▴ 10
1
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3
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364
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 1 day ago by • 0 • written 5 days ago by • 0
0
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2
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186
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
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4 days ago • updated 1 day ago Quang NN ▴ 10
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125
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8 days ago • updated 5 days ago Vinesh • 0
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Unable to find sample sheet file for ChAMP methylation data analysis
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updated 6 days ago by 67k • written 6 days ago by • 0
0
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
7 days ago • updated 5 days ago Blandine • 0
0
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4
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204
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Is there a way to do DEG analysis across two batches sharing one sample only?
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8 days ago • updated 7 days ago georgeyu703 • 0
0
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1
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106
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affymetrix
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updated 8 days ago by 67k • written 9 days ago by • 0
0
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1
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updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
0
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1
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12 days ago • updated 8 days ago ja.garcia • 0
1
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1
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173
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 9 days ago by ▴ 750 • written 12 days ago by • 0
0
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4
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376
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How to sort negative log2FC or FC in RNAseq for GSEA?
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9 days ago • updated 7 days ago Quang NN ▴ 10
2
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4
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351
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updated 5 days ago by 52k • written 10 days ago by • 0
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1
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230
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Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 11 days ago by 43k • written 12 days ago by • 0
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COTAN PCAtools
11 days ago Silvia • 0
1
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2
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Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
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SingleR Label.Ont
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written 16 months ago by • 0
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0
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cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
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12 days ago xiaofeiwang18266 ▴ 50
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5
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717
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109
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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 13 days ago by 67k • written 15 days ago by • 0
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updated 14 days ago by 67k • written 14 days ago by • 0
0
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1
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112
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Unknown gene transcripts after annotatr
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updated 14 days ago by 67k • written 14 days ago by • 0
0
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1
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99
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updated 15 days ago by 67k • written 15 days ago by • 0
0
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0
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16 days ago • updated 15 days ago nurkenber • 0
0
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
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16 days ago GJ • 0
0
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1
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96
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promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
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updated 16 days ago by 67k • written 16 days ago by ▴ 20
0
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0
replies
79
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17 days ago info ▴ 10
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1
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156
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updated 16 days ago by 4.1k • written 18 days ago by • 0
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2
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2
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8
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2
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375
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0
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0
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21 days ago Maggie • 0
1,000 results • Page 1 of 20
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Replies
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
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Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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