Showing : rnaseqdata • reset
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
1
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7
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2.8k
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
2
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9
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4.0k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.4 years ago Peipei • 0
1
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5
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1.8k
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Error in DEseq
DEseq RNASeqData
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
1
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1
reply
1.2k
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NOIseq Probability column
RNAseq RNASeqData NOISeq
3.4 years ago Pratibha ▴ 10
5
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4
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2.6k
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 8 months ago by • 0 • written 3.4 years ago by ▴ 30
0
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2
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2.3k
views
How to run vst transformation
RNASeqData vst
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
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3
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1.9k
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3.5 years ago Maka • 0
0
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5
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3.3k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
3.5 years ago • updated 3.4 years ago priyanka.m • 0
22
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15
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11k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 24 months ago by ▴ 10 • written 3.6 years ago by ▴ 50
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2
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1.6k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 40
3
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2
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1.7k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.6 years ago • updated 3.5 years ago Dakarai ▴ 10
0
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1
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1.2k
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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2
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2.0k
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
3.6 years ago sushimoto • 0
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0
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827
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
3.6 years ago Mafalda • 0
1
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4
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1.6k
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
3.6 years ago sushimoto • 0
0
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0
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1.1k
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3.6 years ago treebig44 ▴ 40
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0
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1.2k
views
high number of reads mapped to too many loci
RNASeqData
3.6 years ago vasa.broz • 0
0
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1
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1.1k
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
3.6 years ago karl.stamm ▴ 10
4
votes
1
reply
3.6k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 40
1
vote
1
reply
988
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 40
4
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6
replies
13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.6 years ago treebig44 ▴ 40
1
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1
reply
3.9k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
1
vote
2
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1.3k
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
3.6 years ago m.glymenaki • 0
1
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1
reply
1.2k
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
4
votes
3
replies
1.9k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by ▴ 10
0
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2
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1.2k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.7 years ago Raito92 ▴ 60
0
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1
reply
2.0k
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
3.7 years ago bas_work ▴ 30
1
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1
reply
2.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
2
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4
replies
1.8k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
4.2 years ago khaveh ▴ 10
0
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2
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1.1k
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
4.3 years ago szomolay • 0
0
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1
reply
1.0k
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Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 4.4 years ago by ▴ 760 • written 4.4 years ago by • 0
0
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3
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1.4k
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 4.4 years ago by ★ 1.4k • written 4.4 years ago by • 0
0
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1
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1.2k
views
t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
4.5 years ago subashika • 0
8
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2
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10k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
4.5 years ago paty ▴ 60
1
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3
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3.2k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
4.5 years ago dantasezequiel1 • 0
1
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15
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3.8k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
4.6 years ago • updated 4.5 years ago demisa • 0
0
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6
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1.8k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
4.6 years ago Rishav ▴ 20
2
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8
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3.8k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 20
3
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4
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2.2k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.6 years ago hgalmoore • 0
7
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4
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17k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 3.8 years ago by • 0 • written 4.6 years ago by ▴ 20
3
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2
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1.3k
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
4.7 years ago Wuschel ▴ 10
1
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6
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2.0k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
4.7 years ago Seaweed • 0
9
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5
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5.2k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
4.9 years ago ecg1g15 ▴ 30
3
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6
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1.8k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
2
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4
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3.6k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
4.9 years ago ecg1g15 ▴ 30
0
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1
reply
888
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
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3
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9.4k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
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1
reply
1.2k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 80
1
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2
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1.9k
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Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 10.8 years ago by ★ 2.1k • written 10.8 years ago by ▴ 150
151 results • Page 3 of 4
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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