Showing : rnaseqdata • reset
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 8 days ago by ★ 2.0k • written 8 days ago by • 0
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1
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66
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Differential RNA seq on TCGA set
DESeq2 RNASeqData
updated 15 days ago by ★ 2.0k • written 15 days ago by • 0
1
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4
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122
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
21 days ago Iwan • 0
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1
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130
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Using DESeq2 for time-series analysis with two conditions
DESeq2 RNASeqData
updated 6 weeks ago by ★ 2.0k • written 6 weeks ago by • 0
0
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1
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122
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
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128
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
4 months ago marymshahi2021 • 0
1
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2
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402
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 4 months ago by ★ 1.2k • written 4 months ago by • 0
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0
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145
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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
5 months ago Pang • 0
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1
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215
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 5 months ago by 47k • written 5 months ago by • 0
1
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7
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470
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 6 months ago by 62k • written 6 months ago by • 0
2
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9
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777
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
7 months ago Peipei • 0
1
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5
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405
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Error in DEseq
DEseq RNASeqData
updated 7 months ago by ★ 2.0k • written 7 months ago by • 0
1
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1
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294
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NOIseq Probability column
RNAseq RNASeqData NOISeq
7 months ago Pratibha ▴ 10
3
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3
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422
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
8 months ago • updated 7 months ago JK Kim ▴ 10
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2
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530
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How to run vst transformation
RNASeqData vst
updated 8 months ago by 39k • written 8 months ago by • 0
2
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3
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479
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
8 months ago Maka • 0
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5
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874
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
9 months ago • updated 8 months ago priyanka.m • 0
22
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14
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3.8k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 8 months ago by • 0 • written 9 months ago by ▴ 50
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2
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531
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Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 9 months ago by 39k • written 9 months ago by ▴ 30
3
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2
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372
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
9 months ago • updated 8 months ago Dakarai ▴ 10
0
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1
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320
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 9 months ago by 39k • written 9 months ago by • 0
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2
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404
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
10 months ago • updated 9 months ago sushimoto • 0
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231
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
10 months ago Mafalda • 0
1
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4
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526
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
10 months ago sushimoto • 0
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0
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271
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
10 months ago treebig44 ▴ 30
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325
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high number of reads mapped to too many loci
RNASeqData
10 months ago vasa.broz • 0
0
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1
reply
236
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
10 months ago karl.stamm ▴ 10
4
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1
reply
717
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 10 months ago by 39k • written 10 months ago by ▴ 30
1
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1
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269
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 10 months ago by 39k • written 10 months ago by ▴ 30
2
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6
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3.8k
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
10 months ago treebig44 ▴ 30
0
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1
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554
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 10 months ago by 47k • written 10 months ago by • 0
1
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2
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334
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
10 months ago m.glymenaki • 0
1
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1
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343
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edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 11 months ago by 47k • written 11 months ago by • 0
3
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3
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497
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 11 months ago by ★ 1.2k • written 11 months ago by • 0
0
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2
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372
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
11 months ago Raito92 ▴ 60
0
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1
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527
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'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
11 months ago bas_work ▴ 10
0
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1
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360
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 15 months ago by 47k • written 15 months ago by • 0
2
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4
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538
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
17 months ago khaveh ▴ 10
0
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2
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451
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
18 months ago szomolay • 0
0
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1
reply
392
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 20 months ago by ▴ 700 • written 20 months ago by • 0
0
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3
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440
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.2k • written 20 months ago by • 0
0
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1
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386
views
t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
21 months ago subashika • 0
6
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2
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3.1k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
21 months ago paty ▴ 40
1
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3
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887
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
21 months ago dantasezequiel1 • 0
1
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15
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1.1k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
21 months ago demisa • 0
0
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6
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655
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while doing co-expression network analysis, I am getting an error
RNASeqData
21 months ago Rishav ▴ 20
2
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8
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923
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 22 months ago by 47k • written 22 months ago by ▴ 20
3
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4
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792
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
22 months ago hgalmoore • 0
6
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4
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4.4k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 12 months ago by • 0 • written 22 months ago by ▴ 10
3
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2
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593
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
23 months ago Wuschel ▴ 10
50 results • Page 1 of 1
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Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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