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2
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1.1k
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Limma - using both array and spot weights in lmFit
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updated 1 day ago by 52k • written 17.6 years ago by ▴ 170
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Margins for gene_set_enrichment_plot
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2 days ago Thomas • 0
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156
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Need new version : tx2gene.gencode.v47.csv
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Deseq2 Design
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updated 3 days ago by 67k • written 3 days ago by • 0
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281
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p value is 0, padj is 0
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3 days ago • updated 2 days ago Wirayatida • 0
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Standardization of rlog transformed counts before PCA
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Cannot install GO.db and org.Hs.eg.db
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Help using rtracklayer for gene ID extraction
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Feature Counts - potential bug with outfile.jcounts
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updated 3 days ago by ★ 3.6k • written 5 days ago by • 0
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353
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
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4 days ago • updated 3 days ago georgii.vdovin • 0
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440
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Feature Counts -R XS Read Assignment Tag
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updated 3 days ago by 52k • written 9 months ago by • 0
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4 days ago txema.heredia • 0
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MEDIPS for chIP-Seq
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Matching patterns in an AAStringset
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updated 5 days ago by ▴ 60 • written 5 days ago by • 0
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
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5 days ago • updated 4 days ago Tadeoye ▴ 20
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623
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
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updated 4 days ago by • 0 • written 6 days ago by • 0
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4
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210
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Can we get beta values with DMRcate package
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6 days ago • updated 4 days ago Melisa Tecik • 0
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Running multiple KNN queries in parallel
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9 days ago • updated 7 days ago SamGG ▴ 360
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RSubread output significantly different from bash Subread output
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updated 5 days ago by ★ 4.6k • written 9 days ago by • 0
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
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updated 8 days ago by 43k • written 9 days ago by ▴ 20
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408
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sva: get a sv for RIN scores
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updated 8 days ago by 52k • written 9 days ago by ▴ 10
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git push errors
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10 days ago Jiping Wang ▴ 90
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3
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How to annotate a limma Elist raw class object with an annotation file
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318
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DESeq2 - Comparing Comparisons
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updated 4 days ago by 67k • written 11 days ago by • 0
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75
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Confidence interval contains 0 but p<0.05
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11 days ago Adelyn • 0
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4
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16 days ago • updated 11 days ago cropero • 0
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Pathway abundance data from Curatedmetagenomics
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11 days ago Edward • 0
1
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4
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pathview - multiple states
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12 days ago • updated 11 days ago Philippine • 0
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scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
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updated 10 days ago by ★ 28k • written 13 days ago by ▴ 10
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2
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contrast matrix design for a continuous variable
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12 days ago dtzhu337 • 0
1
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207
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DESeq2- merging technical vs biological replicates
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updated 12 days ago by 43k • written 20 days ago by • 0
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updated 12 days ago by 43k • written 13 days ago by • 0
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fail to use addPerROIQC in Rmd
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updated 12 days ago by • 0 • written 13 days ago by • 0
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how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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13 days ago xiaofeiwang198266 • 0
3
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Crossover design with limma
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Differential Expression Genes as Independent Variables
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updated 10 days ago by 67k • written 16 days ago by • 0
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rrvgo::calculateSimMatrix() error
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updated 13 days ago by • 0 • written 17 days ago by • 0
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18 days ago Daphne • 0
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DESeq2 sizefactors counfounded with biological treatment
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18 days ago Anna • 0
2
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1
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220
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bioconductor packages on bioconda
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updated 19 days ago by 67k • written 19 days ago by • 0
1
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4
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txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
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19 days ago • updated 18 days ago remi-xavier.coux ▴ 10
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Epic v2 Annotation CpG_maf source?
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20 days ago • updated 18 days ago Meghan • 0
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Struggle with the replicates of epic array data
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written 22 days ago by • 0
0
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0
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93
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
20 days ago David R ▴ 90
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0
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Spam: <img/src/onerror=alert&#xFEFF;(1337)>
genomes rgu34cprobe
22 days ago <img/src/onerror=alert&#xFEFF;(1337)> 0
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Answer: Limma - using both array and spot weights in lmFit by Gordon Smyth 52k
Was answered here: https://support.bioconductor.org/p/17028/
Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label by daldabrown9 • 0
For more info visit us on [R350 status check][1] [1]: https://sassagrantstatuscheck.co.za/
Answer: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Maria please read the mirTarRnaSeq paper. In particular, Supplemental Table 2, clarifies all the statistical models, inputs and outputs. If…
Comment: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
Fold change calculation in Diffbind vs. DESEQ2?
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
Answer: FeatureCounts Output Counts at Exon Level Using Default Settings, want gene leve
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
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