Showing : RNASeqData • reset
0
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2
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115
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How to run vst transformation
RNASeqData vst
updated 8 days ago by 36k • written 13 days ago by • 0
2
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3
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151
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
17 days ago • updated 16 days ago Maka • 0
0
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2
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115
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
4 weeks ago priyanka.m • 0
21
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14
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1.2k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 13 days ago by • 0 • written 5 weeks ago by ▴ 50
0
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2
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137
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Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 5 weeks ago by 36k • written 5 weeks ago by ▴ 30
3
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2
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127
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
6 weeks ago • updated 16 days ago Dakarai ▴ 10
0
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1
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122
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 6 weeks ago by 36k • written 6 weeks ago by • 0
0
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2
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155
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
7 weeks ago • updated 6 weeks ago sushimoto • 0
0
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0
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86
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
7 weeks ago Mafalda • 0
1
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4
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189
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
7 weeks ago sushimoto • 0
0
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0
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83
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
7 weeks ago treebig44 ▴ 30
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0
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75
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high number of reads mapped to too many loci
RNASeqData
7 weeks ago vasa.broz • 0
0
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1
reply
80
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
8 weeks ago karl.stamm ▴ 10
4
votes
1
reply
174
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 8 weeks ago by 36k • written 8 weeks ago by ▴ 30
1
vote
1
reply
102
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 9 weeks ago by 36k • written 9 weeks ago by ▴ 30
2
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6
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250
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
9 weeks ago treebig44 ▴ 30
0
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1
reply
157
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 10 weeks ago by 45k • written 10 weeks ago by • 0
1
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2
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154
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
10 weeks ago • updated 7 weeks ago m.glymenaki • 0
1
vote
1
reply
165
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 12 weeks ago by 45k • written 12 weeks ago by • 0
1
vote
3
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241
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 12 weeks ago by ★ 1.0k • written 12 weeks ago by • 0
0
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2
replies
221
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3 months ago Raito92 ▴ 60
0
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1
reply
181
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
3 months ago bas_work ▴ 10
0
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1
reply
209
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 6 months ago by 45k • written 6 months ago by • 0
2
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4
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296
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
8 months ago khaveh ▴ 10
0
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2
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267
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
9 months ago szomolay • 0
0
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1
reply
249
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 11 months ago by ▴ 660 • written 11 months ago by • 0
0
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3
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288
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 11 months ago by ★ 1.0k • written 11 months ago by • 0
0
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1
reply
234
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t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
12 months ago subashika • 0
3
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2
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1.5k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
12 months ago paty ▴ 20
1
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3
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533
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
13 months ago dantasezequiel1 • 0
1
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15
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752
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
13 months ago demisa • 0
0
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6
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428
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while doing co-expression network analysis, I am getting an error
RNASeqData
13 months ago Rishav ▴ 20
2
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8
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620
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 13 months ago by 45k • written 13 months ago by ▴ 20
3
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4
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547
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
13 months ago hgalmoore • 0
4
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4
replies
2.3k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 4 months ago by • 0 • written 14 months ago by ▴ 10
3
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2
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426
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
15 months ago Wuschel ▴ 10
1
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6
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484
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
15 months ago Seaweed • 0
7
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5
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893
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
18 months ago • updated 17 months ago ecg1g15 • 0
3
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6
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637
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 17 months ago by 36k • written 18 months ago by ▴ 50
2
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4
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859
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
18 months ago ecg1g15 • 0
0
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1
reply
252
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 18 months ago by 3.5k • written 18 months ago by • 0
0
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3
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3.2k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 18 months ago by 59k • written 18 months ago by • 0
0
votes
1
reply
823
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 6.1 years ago by 36k • written 6.1 years ago by ▴ 70
1
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2
replies
1.1k
views
Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 7.3 years ago by ★ 1.9k • written 7.3 years ago by ▴ 150
0
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10
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2.0k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 7.9 years ago by ▴ 320 • written 7.9 years ago by ★ 6.7k
45 results • Page 1 of 1
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Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Yang Shi • 0
Got that sir, thanks so much!
Comment: UniprotKB AC/ID to Entrez ID Conversion by Guido Hooiveld ★ 3.2k
No, no need to modify `up`. It somehow has to do with the R.BioC version; it works when using the latest versions (R-4.2.0/BioC-3.15), but…
Comment: UniprotKB AC/ID to Entrez ID Conversion by tom.kloter • 0
Thanks a lot for your response! I tried the code in my script and got to the following result: ``` > up <- UniProt.ws(taxId=9606) > up "U…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Guido Hooiveld ★ 3.2k
Regarding the normalization method (SCAN); I have only used RMA for the reasons James explained in one of your other threads (https://suppo…
Answer: UniprotKB AC/ID to Entrez ID Conversion by Guido Hooiveld ★ 3.2k
The key to realize is that your input is a vector of Uniprot **ID**s (also known as 'entry names') . The central identifier in the Uniprot …
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
A: coefficient not estimable (limma warning)
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