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15
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Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
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GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 11 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
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6 months ago • updated 2 days ago shepherl 3.8k
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5
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featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
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updated 9 months ago by ▴ 380 • written 2.8 years ago by ▴ 10
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Genelist input for ClusterProfiler
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updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
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When is centering and scaling needed before doing hierarchical clustering?
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written 6.7 years ago by ▴ 20
2
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Installing Local packages in Bioconductor
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updated 8 months ago by • 0 • written 23 months ago by • 0
1
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Problems Installing biomaRt
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updated 5 months ago by 65k • written 2.0 years ago by ▴ 20
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How to get DESeq2 sizefactors from data imported using tximport
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updated 11 months ago by • 0 • written 6.8 years ago by • 0
2
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Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
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updated 4 months ago by 65k • written 16 months ago by ▴ 10
5
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How to annotate gene names for genomic coordinates?
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written 8.8 years ago by • 0
0
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3
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4.1k
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The MicrobiotaProcess package performed lefse analysis and had a problem drawing the tree
MicrobiotaProcess offspring.tbl_tree_item
updated 9 months ago by • 0 • written 9 months ago by • 0
6
votes
5
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DESeq2: Extremely low pvalues
deseq2
updated 9 months ago by 65k • written 7.8 years ago by ▴ 20
2
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2
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choosing the normalization method (rlog, variance stabilizing transformation)
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updated 5 months ago by • 0 • written 6.4 years ago by ▴ 80
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Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 6 months ago by 690 • written 20 months ago by ▴ 20
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Bgratio column in clusterProfiler enrichGO results
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updated 9 months ago by • 0 • written 7.8 years ago by ▴ 10
6
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11
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How to properly average normalized counts of biological replicates
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updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 40
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Problem about picking soft threshold power in WGCNA software
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written 7.1 years ago by ▴ 40
10
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8
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conumee error: query intensities not given for all probes.
conumee
updated 3 months ago by • 0 • written 6.8 years ago by ▴ 30
2
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4
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How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 10 weeks ago by 50k • written 4.7 years ago by • 0
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5
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PCA plot for TPM data
PCA
written 6.5 years ago by ▴ 20
5
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6
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Differential protein/biomarker expression using limma: is that possible?
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updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
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4
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SingleR Label.Ont
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updated 8 days ago by • 0 • written 7 months ago by • 0
4
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4
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Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 4 weeks ago by • 0 • written 6.4 years ago by ▴ 20
4
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12
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Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 6 months ago by • 0 • written 3.2 years ago by • 0
0
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11
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bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 12 weeks ago by ▴ 170 • written 7.1 years ago by ★ 2.0k
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4
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error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
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updated 10 months ago by • 0 • written 4.4 years ago by • 0
0
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2
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Dealing with multi-overlapping and multi-mapping reads
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written 3.8 years ago by ▴ 80
1
vote
4
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ggtree functions suddenly stopped working: "Error in offspring.tbl_tree_item(..."
ggtree
updated 9 months ago by • 0 • written 9 months ago by • 0
4
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14
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Data input for aracne2regulon function in viper package
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updated 3 months ago by • 0 • written 4.7 years ago by ▴ 30
0
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17
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What causes this DESeq2 error at "fitting model and testing"?
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updated 10 months ago by • 0 • written 6.6 years ago by • 0
1
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11
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Error: Bioconductor version cannot be validated; no internet connection?
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updated 5 months ago by • 0 • written 9 months ago by • 0
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Best way to handle tags of bam files
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Bioconductor version cannot be validated
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updated 7 months ago by 65k • written 7 months ago by • 0
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SRAdb: Error downloading sqlite files
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written 6.5 years ago by • 0
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3
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ASpli: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': 'start' or 'end' canno…
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updated 7 months ago by • 0 • written 18 months ago by • 0
1
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8
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Normalization starting from beta values in minfi
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written 7.9 years ago by ▴ 290
1
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16
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error in ChAMP loading file
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updated 6 weeks ago by • 0 • written 17 months ago by • 0
4
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How to find the amino acid codon corresponding to a translated genomic position
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updated 3 months ago by ▴ 10 • written 8.4 years ago by ▴ 10
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DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by 41k • written 5.7 years ago by ▴ 20
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5
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How to use EnrichGo of Cluster Profiler
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written 3.3 years ago by • 0
0
votes
6
replies
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limma, analysis on subset of data gives completely different results
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updated 22 days ago by 50k • written 9.8 years ago by ▴ 40
0
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clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.1 years ago by • 0
2
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9
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NCBI Locus ID to gene ID conversion
LocusIDtogeneIDconversion
updated 5 months ago by • 0 • written 20 months ago by ▴ 20
2
votes
3
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3.1k
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Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.7 years ago by ▴ 50
1
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2
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Extract genes from ggvenn?
ggvenn
updated 18 days ago by ▴ 10 • written 24 months ago by • 0
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views
Problems with FLOWAI
flowAI
written 3.0 years ago by • 0
1
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3
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maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
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updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ▴ 100
3
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4
replies
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Collecting unmapped RNA-seq reads
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written 4.6 years ago by • 0
2
votes
6
replies
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DESeq2 Dispersion Per Condition
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updated 9 months ago by • 0 • written 8.0 years ago by ▴ 20
1,749 results • Page 2 of 35
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Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Comment: Different Shrunk Log2FC according with reference by Michael Love 41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
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an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
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Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
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Reproducibility issue with scran together with lapply and BiocParallel
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