Showing : rnaseqdata • reset
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Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
17 days ago Pang • 0
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1
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94
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 18 days ago by 46k • written 18 days ago by • 0
1
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7
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238
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 5 weeks ago by 60k • written 5 weeks ago by • 0
2
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9
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357
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
8 weeks ago Peipei • 0
1
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5
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193
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Error in DEseq
DEseq RNASeqData
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
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1
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115
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NOIseq Probability column
RNAseq RNASeqData NOISeq
10 weeks ago • updated 9 weeks ago Pratibha • 0
3
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3
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243
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
11 weeks ago JK Kim ▴ 10
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2
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238
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How to run vst transformation
RNASeqData vst
updated 3 months ago by 37k • written 3 months ago by • 0
2
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3
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267
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3 months ago Maka • 0
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5
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460
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
4 months ago • updated 11 weeks ago priyanka.m • 0
22
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14
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2.3k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 3 months ago by • 0 • written 4 months ago by ▴ 50
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2
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227
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Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 4 months ago by 37k • written 4 months ago by ▴ 30
3
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2
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222
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
4 months ago • updated 3 months ago Dakarai ▴ 10
0
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1
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200
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 4 months ago by 37k • written 4 months ago by • 0
0
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2
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243
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
4 months ago sushimoto • 0
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0
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134
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
4 months ago Mafalda • 0
1
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4
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357
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
4 months ago sushimoto • 0
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0
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155
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
4 months ago treebig44 ▴ 30
0
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0
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166
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high number of reads mapped to too many loci
RNASeqData
4 months ago vasa.broz • 0
0
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1
reply
131
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
5 months ago karl.stamm ▴ 10
4
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1
reply
279
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 5 months ago by 37k • written 5 months ago by ▴ 30
1
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1
reply
152
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 5 months ago by 37k • written 5 months ago by ▴ 30
2
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6
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517
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
5 months ago treebig44 ▴ 30
0
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1
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274
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 5 months ago by 46k • written 5 months ago by • 0
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2
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219
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
5 months ago • updated 4 months ago m.glymenaki • 0
1
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1
reply
225
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edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 5 months ago by 46k • written 5 months ago by • 0
1
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3
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308
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 5 months ago by ★ 1.1k • written 5 months ago by • 0
0
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2
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275
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
6 months ago Raito92 ▴ 60
0
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1
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302
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'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
6 months ago bas_work ▴ 10
0
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1
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252
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 9 months ago by 46k • written 9 months ago by • 0
2
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4
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350
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
11 months ago khaveh ▴ 10
0
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2
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338
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
12 months ago szomolay • 0
0
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1
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292
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Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 14 months ago by ▴ 690 • written 14 months ago by • 0
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3
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334
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 14 months ago by ★ 1.1k • written 14 months ago by • 0
0
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1
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287
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t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
15 months ago subashika • 0
6
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2
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2.1k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
15 months ago paty ▴ 40
1
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3
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649
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
16 months ago dantasezequiel1 • 0
1
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15
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872
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
16 months ago demisa • 0
0
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6
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498
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while doing co-expression network analysis, I am getting an error
RNASeqData
16 months ago Rishav ▴ 20
2
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8
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716
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 16 months ago by 46k • written 16 months ago by ▴ 20
3
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4
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634
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
16 months ago hgalmoore • 0
6
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4
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3.0k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 7 months ago by • 0 • written 17 months ago by ▴ 10
3
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2
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479
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
18 months ago Wuschel ▴ 10
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6
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560
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
18 months ago Seaweed • 0
7
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5
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1.1k
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Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
21 months ago • updated 20 months ago ecg1g15 • 0
3
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6
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692
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 20 months ago by 37k • written 21 months ago by ▴ 50
2
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4
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970
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Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
21 months ago ecg1g15 • 0
0
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1
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291
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RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 21 months ago by 3.6k • written 21 months ago by • 0
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3
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3.9k
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Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 21 months ago by 60k • written 21 months ago by • 0
0
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1
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852
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 6.3 years ago by 37k • written 6.4 years ago by ▴ 70
50 results • Page 1 of 1
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Replies
Answer: Design and contrast matrices for analyzing the effect of two factors of interest by Gordon Smyth 46k
> In a typical regression, I would just add them to the model when estimating my coefficients of interest Why not do the same with limma? …
Comment: TPM normalization starting with read counts by Gordon Smyth 46k
> So you think my method in TPM normalization that I introduced above is not good? Your computation of RPKM using edgeR is fine, provided …
Comment: error in package GenVisR while installing by 堃 • 0
Package ‘FField’ was removed from the CRAN repository.[enter link description here][1] I installed FField by using remotes::install_github…
Comment: DESeq 2 failes to load by Ruggero • 0
This solved the error, in case someone else is having compilation errors from installing RSQllite: install.packages('RSQLite', repos='http…
Comment: pathview says my nonmodel species is unknown: "species invalid" by Guido Hooiveld ★ 3.3k
A while ago a faced the same for another non-model organism. I was able to get it working using a 'hack'. This hack is nothing more than m…
Votes
DiffBind affinity vs occupancy Heatmaps
Answer: How to remove dendrogram from pheatmaps?
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: How to select summit size for histone ChiP-Seq in Diffbind
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