14
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5
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22k
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Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
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10
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Archives prior to 3.15 gone
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updated 6 months ago by 3.9k • written 20 months ago by ▴ 30
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17
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.6 years ago by • 0
1
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5
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2.2k
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pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.3 years ago by ▴ 10
2
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2
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405
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"Details" section for specific software packages
Website
updated 7 months ago by ★ 6.5k • written 7 months ago by • 0
2
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3
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2.2k
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Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 12 months ago by 16k • written 12 months ago by ▴ 20
0
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18
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2.6k
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problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
0
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2
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238
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WGCNA: analysis of complex trait associations with regressions
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7 weeks ago • updated 6 weeks ago w.cookson • 0
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9
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
8
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7
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
0
votes
4
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648
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
9 months ago anne.hoffrichter • 0
4
votes
9
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1.4k
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DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 9 months ago by ▴ 10 • written 9 months ago by ▴ 10
0
votes
2
replies
566
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
4
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4
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3.5k
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Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
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0
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2
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878
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Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by 42k • written 9 months ago by • 0
6
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5
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6.3k
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Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
0
votes
2
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497
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plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
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6
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1.5k
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How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 6 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
1
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2
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708
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DESeq2 batch design
DESeq2
updated 8 months ago by ★ 1.4k • written 9 months ago by ▴ 10
4
votes
7
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896
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weird volcano plot
DESeq2
updated 10 weeks ago by • 0 • written 6 months ago by ▴ 10
0
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5
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2.9k
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DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 11 days ago Henrik Bengtsson ★ 2.4k
0
votes
2
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303
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
2
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329
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locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
11 weeks ago Hope ▴ 10
7
votes
6
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4.2k
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Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 7 months ago by 700 • written 21 months ago by ▴ 20
2
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5
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1.4k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
2
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157
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DESeq2 v1.35.0
DESeq2
updated 14 days ago by 42k • written 14 days ago by • 0
3
votes
3
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413
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plotUMAP Gene Set Faceted
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
2
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3
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3.1k
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Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by ▴ 50
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3
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 16 days ago by • 0 • written 13.1 years ago by ▴ 10
28
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21
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49k
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deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.2 years ago by ▴ 40
1
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3
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498
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DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
3
replies
373
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Sign Output Values PADOG
PADOG
updated 6 months ago by • 0 • written 6 months ago by • 0
1
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6
replies
759
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Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 11 weeks ago by 65k • written 3 months ago by • 0
2
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8
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1.1k
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Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
0
votes
4
replies
394
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Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
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3
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1.9k
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Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 months ago by • 0
6
votes
19
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2.6k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
0
votes
2
replies
349
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Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
votes
6
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916
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
1
vote
7
replies
6.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 10 weeks ago by 16k • written 6 months ago by ▴ 10
5
votes
5
replies
467
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create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago baptiste ▴ 20
0
votes
5
replies
9.3k
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tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 8 weeks ago by • 0 • written 7.6 years ago by • 0
6
votes
7
replies
968
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[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 7 months ago by ▴ 20
4
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2
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Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
1
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2
replies
286
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Problems with Feature counting
Rsubread BAMfiles GTFfile
3 months ago mirjanakessler • 0
0
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3
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1.4k
views
An ESR essay about software design, and how it applies to Bioconductor
GUI GUI
written 20.2 years ago by ▴ 50
1
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5
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881
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
1
vote
5
replies
619
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Errors with makeTxDbFromBiomart
biomaRt
updated 9 months ago by 65k • written 9 months ago by ▴ 10
3
votes
2
replies
463
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by 50k • written 10 months ago by • 0
1,000 results • Page 2 of 20
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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