Showing : RNASeqData • reset
3
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11
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1.8k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 months ago by • 0
3
votes
2
replies
1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 12 weeks ago by ▴ 20
0
votes
1
reply
704
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
1
vote
1
reply
361
views
Merging annotation with differential expression output
annotation RNASeqData
updated 5 months ago by 68k • written 5 months ago by • 0
0
votes
3
replies
817
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
0
replies
263
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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
7 months ago cftattersfield • 0
0
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5
replies
600
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 7 months ago by • 0
0
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1
reply
389
views
Correlation between gene clusters
genomes RNASeqData
written 7 months ago by • 0
0
votes
2
replies
575
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
7 months ago gingergeiger22 • 0
2
votes
1
reply
568
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
503
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 8 months ago by • 0 • written 8 months ago by • 0
2
votes
1
reply
642
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
4
replies
950
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
10 months ago Philippine • 0
0
votes
2
replies
682
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 10 months ago by • 0
1
vote
1
reply
794
views
WGCNA
DEGselection RNASeqData WGCNA
updated 10 months ago by ▴ 760 • written 10 months ago by • 0
1
vote
1
reply
501
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
1
vote
1
reply
782
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 12 months ago by 52k • written 12 months ago by • 0
1
vote
2
replies
2.9k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 12 months ago by • 0
1
vote
2
replies
605
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
12 months ago Gordon • 0
0
votes
3
replies
888
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
0
votes
4
replies
977
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 13 months ago by • 0
1
vote
3
replies
1.8k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
14 months ago Tanvi • 0
1
vote
3
replies
905
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 14 months ago by 68k • written 14 months ago by ▴ 50
0
votes
1
reply
586
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
1
reply
606
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 12 months ago by ▴ 20 • written 15 months ago by • 0
0
votes
1
reply
588
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 months ago by 52k • written 16 months ago by • 0
0
votes
1
reply
576
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 17 months ago by 68k • written 17 months ago by • 0
3
votes
5
replies
1.6k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 18 months ago by 43k • written 18 months ago by ▴ 10
0
votes
0
replies
714
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
18 months ago Abril • 0
1
vote
2
replies
2.3k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.3 years ago by • 0
1
vote
3
replies
1.1k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
19 months ago island • 0
0
votes
2
replies
746
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
19 months ago Diana • 0
0
votes
1
reply
1.1k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 19 months ago by ★ 4.9k • written 19 months ago by • 0
5
votes
6
replies
1.4k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
19 months ago Shaimaa Gamal • 0
1
vote
1
reply
891
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 20 months ago by ★ 4.9k • written 20 months ago by • 0
0
votes
2
replies
1.1k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
20 months ago Luca • 0
0
votes
1
reply
1.6k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
2
replies
1.1k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
21 months ago drewhaydensteele • 0
1
vote
1
reply
877
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 21 months ago by ★ 4.9k • written 21 months ago by • 0
1
vote
2
replies
1.7k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
21 months ago • updated 20 months ago Levi • 0
0
votes
3
replies
2.5k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
21 months ago Oenone • 0
3
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4
replies
1.3k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
21 months ago pl23 • 0
0
votes
1
reply
725
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
votes
2
replies
968
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
21 months ago Manthos • 0
0
votes
1
reply
833
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 21 months ago by ★ 13k • written 22 months ago by • 0
0
votes
2
replies
899
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
22 months ago Ben ▴ 10
0
votes
2
replies
2.5k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
22 months ago RHEA • 0
2
votes
3
replies
2.5k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 22 months ago by ★ 1.4k • written 22 months ago by • 0
1
vote
1
reply
976
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
1
vote
7
replies
1.7k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 21 months ago by 52k • written 23 months ago by • 0
150 results • Page 1 of 3
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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