Showing : rnaseqdata • reset
3
votes
6
replies
709
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 25 days ago by • 0
0
votes
2
replies
443
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 15 days ago by • 0 • written 12 weeks ago by • 0
3
votes
13
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2.2k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 14 months ago by • 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 6 months ago by ▴ 20
0
votes
1
reply
772
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
1
vote
1
reply
439
views
Merging annotation with differential expression output
annotation RNASeqData
updated 8 months ago by 68k • written 8 months ago by • 0
0
votes
3
replies
1.0k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
359
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
10 months ago cftattersfield • 0
0
votes
5
replies
735
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 months ago by • 0
0
votes
1
reply
474
views
Correlation between gene clusters
genomes RNASeqData
written 11 months ago by • 0
0
votes
2
replies
724
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 months ago gingergeiger22 • 0
2
votes
1
reply
734
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
634
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 11 months ago by • 0 • written 11 months ago by • 0
2
votes
1
reply
727
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
13 months ago Philippine • 0
0
votes
2
replies
808
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 13 months ago by • 0
1
vote
1
reply
989
views
WGCNA
DEGselection RNASeqData WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
1
vote
1
reply
710
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
1
reply
871
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
2
replies
3.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 15 months ago by • 0
1
vote
2
replies
701
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
15 months ago Gordon • 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 17 months ago by • 0
1
vote
3
replies
1.9k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
18 months ago Tanvi • 0
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 18 months ago by 68k • written 18 months ago by ▴ 50
0
votes
1
reply
651
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
1
reply
740
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 15 months ago by ▴ 20 • written 19 months ago by • 0
0
votes
1
reply
659
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
0
votes
1
reply
666
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 20 months ago by 68k • written 20 months ago by • 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 22 months ago by ▴ 10
0
votes
0
replies
773
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
22 months ago Abril • 0
1
vote
2
replies
2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
22 months ago island • 0
0
votes
2
replies
848
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
22 months ago Diana • 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
5
votes
6
replies
1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
23 months ago Shaimaa Gamal • 0
1
vote
1
reply
982
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
0
votes
2
replies
1.2k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
2.0 years ago Luca • 0
0
votes
1
reply
1.7k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
1
vote
2
replies
1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.0 years ago drewhaydensteele • 0
1
vote
1
reply
964
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
1
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.0 years ago • updated 24 months ago Levi • 0
0
votes
3
replies
2.7k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
2.0 years ago Oenone • 0
3
votes
4
replies
1.4k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.1 years ago pl23 • 0
0
votes
1
reply
799
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.1 years ago Manthos • 0
0
votes
1
reply
899
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.1 years ago by ★ 13k • written 2.1 years ago by • 0
0
votes
2
replies
993
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.1 years ago Ben ▴ 10
0
votes
2
replies
2.6k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
2.1 years ago RHEA • 0
2
votes
3
replies
2.7k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
152 results • Page 1 of 4
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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