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
3.5 years ago Pang • 0
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1
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1.1k
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
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7
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3.0k
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
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9
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4.3k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.6 years ago Peipei • 0
1
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5
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1.9k
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Error in DEseq
DEseq RNASeqData
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
1
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1
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1.2k
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NOIseq Probability column
RNAseq RNASeqData NOISeq
3.7 years ago • updated 3.6 years ago Pratibha ▴ 10
5
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4
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2.8k
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 11 months ago by • 0 • written 3.7 years ago by ▴ 30
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2
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2.4k
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How to run vst transformation
RNASeqData vst
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
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3
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2.0k
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3.7 years ago Maka • 0
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5
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3.5k
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
3.8 years ago • updated 3.7 years ago priyanka.m • 0
22
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15
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12k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 2.2 years ago by ▴ 10 • written 3.8 years ago by ▴ 50
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2
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1.6k
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Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 40
3
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2
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1.8k
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.8 years ago • updated 3.7 years ago Dakarai ▴ 10
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1
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1.3k
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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2
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2.2k
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
3.8 years ago sushimoto • 0
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0
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879
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
3.8 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
3.8 years ago sushimoto • 0
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0
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1.1k
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3.8 years ago treebig44 ▴ 40
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0
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1.3k
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high number of reads mapped to too many loci
RNASeqData
3.8 years ago vasa.broz • 0
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1
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1.2k
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
3.9 years ago karl.stamm ▴ 10
4
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1
reply
3.9k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 40
1
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1
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1.0k
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 40
4
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6
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13k
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.9 years ago treebig44 ▴ 40
1
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1
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4.2k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
1
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2
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1.5k
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
3.9 years ago • updated 3.8 years ago m.glymenaki • 0
1
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1
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1.3k
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
4
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3
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2.1k
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 3.9 years ago by ★ 1.4k • written 3.9 years ago by ▴ 10
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2
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1.3k
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
4.0 years ago Raito92 ▴ 60
0
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1
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2.2k
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'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
4.0 years ago bas_work ▴ 30
1
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1
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2.2k
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
2
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4
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1.9k
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
4.4 years ago khaveh ▴ 10
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2
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1.2k
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
4.5 years ago szomolay • 0
0
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1
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1.1k
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Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 4.7 years ago by ▴ 760 • written 4.7 years ago by • 0
0
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3
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1.5k
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 4.7 years ago by ★ 1.4k • written 4.7 years ago by • 0
0
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1
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1.3k
views
t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
4.8 years ago • updated 4.7 years ago subashika • 0
8
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2
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11k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
4.8 years ago paty ▴ 60
1
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3
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3.5k
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
4.8 years ago dantasezequiel1 • 0
1
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15
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4.0k
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
4.8 years ago demisa • 0
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6
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1.9k
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while doing co-expression network analysis, I am getting an error
RNASeqData
4.8 years ago Rishav ▴ 20
2
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8
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4.0k
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 20
3
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4
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2.4k
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.8 years ago hgalmoore • 0
7
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4
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18k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 4.1 years ago by • 0 • written 4.9 years ago by ▴ 20
3
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2
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1.4k
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
4.9 years ago Wuschel ▴ 10
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6
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2.2k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
5.0 years ago Seaweed • 0
9
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5
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5.5k
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Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
5.2 years ago ecg1g15 ▴ 30
3
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6
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1.9k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 50
2
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4
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3.8k
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Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
5.2 years ago ecg1g15 ▴ 30
0
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1
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932
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
0
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3
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9.7k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
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1
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1.3k
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 80
152 results • Page 3 of 4
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Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
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Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
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