Showing : rnaseqdata • reset
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 21 days ago by 43k • written 6 weeks ago by • 0
3
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11
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2.0k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 months ago by • 0
3
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2
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1.4k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
0
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1
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733
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
1
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1
reply
410
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Merging annotation with differential expression output
annotation RNASeqData
updated 7 months ago by 68k • written 7 months ago by • 0
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3
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939
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
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0
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326
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My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
9 months ago cftattersfield • 0
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5
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682
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 months ago by • 0
0
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1
reply
434
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Correlation between gene clusters
genomes RNASeqData
written 9 months ago by • 0
0
votes
2
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663
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
10 months ago • updated 9 months ago gingergeiger22 • 0
2
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1
reply
643
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
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575
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 10 months ago by • 0 • written 10 months ago by • 0
2
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1
reply
682
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 11 months ago by 43k • written 11 months ago by • 0
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4
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1.1k
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
12 months ago Philippine • 0
0
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2
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754
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 12 months ago by • 0
1
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1
reply
879
views
WGCNA
DEGselection RNASeqData WGCNA
updated 12 months ago by ▴ 760 • written 12 months ago by • 0
1
vote
1
reply
596
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
vote
1
reply
841
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 14 months ago by 53k • written 14 months ago by • 0
1
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2
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3.0k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 14 months ago by • 0
1
vote
2
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654
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
14 months ago Gordon • 0
0
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3
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962
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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4
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1.1k
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 15 months ago by • 0
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3
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1.9k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
16 months ago Tanvi • 0
1
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3
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990
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 16 months ago by 68k • written 16 months ago by ▴ 50
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1
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630
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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1
reply
683
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 14 months ago by ▴ 20 • written 17 months ago by • 0
0
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1
reply
627
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
1
reply
636
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 19 months ago by 68k • written 19 months ago by • 0
3
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5
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1.7k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
0
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0
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744
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
20 months ago Abril • 0
1
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2
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2.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.5 years ago by • 0
1
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3
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1.2k
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
21 months ago island • 0
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2
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806
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
21 months ago Diana • 0
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1
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1.1k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
5
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6
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1.5k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
21 months ago Shaimaa Gamal • 0
1
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1
reply
946
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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2
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1.2k
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
22 months ago Luca • 0
0
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1
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1.7k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
1
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2
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1.1k
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
23 months ago drewhaydensteele • 0
1
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1
reply
926
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
1
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2
replies
1.8k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
23 months ago • updated 22 months ago Levi • 0
0
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3
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2.6k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
23 months ago Oenone • 0
3
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4
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1.4k
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
23 months ago pl23 • 0
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1
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770
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 23 months ago by 43k • written 23 months ago by ▴ 10
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2
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1.1k
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
23 months ago Manthos • 0
0
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1
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868
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 23 months ago by ★ 13k • written 24 months ago by • 0
0
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2
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945
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
24 months ago Ben ▴ 10
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2
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2.6k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
24 months ago RHEA • 0
2
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3
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2.6k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
1
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1
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1.0k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
151 results • Page 1 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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