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9
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2.2k
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Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
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2.7 years ago raf4 ▴ 30
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Is this DESeq2 interactions design correct?
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8
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Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
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how to match salmon output to txname
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Online Venn diagram generator where I can paste text files containing gene name lists to get the diagram
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updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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Help for RNA sequencing analysis with DESEQ2
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updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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Combining VST counts for replicates
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How to handle multiple assay versions in a ChipDb annotation package
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updated 2.6 years ago by 68k • written 2.7 years ago by • 0
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How to set threshold of padj value in DeSeq2
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
3
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Why is it better to count genes at the exon-level using subread::featureCounts()?
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updated 2.7 years ago by 53k • written 2.7 years ago by • 0
5
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Problem obtaining NCBI gene IDs from Ensembl version 107
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2.7 years ago Tess • 0
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1
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Differential RNA seq on TCGA set
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updated 2.7 years ago by ★ 4.9k • written 2.7 years ago by • 0
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2.7 years ago Lluís Revilla Sancho ▴ 760
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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adding peptides to a multiple sequence alignment
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2.7 years ago Mario Dejung • 0
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rlog() transformation works only when using DESeqDataSet, not matrix
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7
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2.7 years ago francesco.gandolfi • 0
1
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0
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
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2.7 years ago Arend ▴ 10
0
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974
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Error in ATACseqQC bamQC analysis
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written 2.7 years ago by ▴ 10
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1
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cell_count column in SpatialExperiment Object
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updated 2.6 years ago by ▴ 160 • written 2.7 years ago by ▴ 10
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Diffbind matrix/batch effect/normalization
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updated 2.7 years ago by ★ 5.2k • written 2.8 years ago by ▴ 10
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2.7 years ago vm ▴ 30
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Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
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updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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0
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8
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Question about Diffbind counts
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2.7 years ago • updated 2.6 years ago slrpatty • 0
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3
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Minor issue regarding customization of text size in Volcano and Heatmap Plots
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updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 10
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Missing transcript
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updated 2.7 years ago by ★ 4.9k • written 2.7 years ago by • 0
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3
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Some discrepancy between ED genes in cBioPortal vs DESeq2
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2.7 years ago Alexandre • 0
0
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1
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740
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dba.count Error in DiffBind
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2.7 years ago narzouni • 0
1
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4
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
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2.7 years ago stacy.genovese • 0
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Inverted Log2FC values after DEseq2 analysis
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2.7 years ago Iwan • 0
46,617 results • Page 64 of 933
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Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
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Answer: Limpa Pipeline Order
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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