Showing : rnaseqdata • reset
0
votes
1
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102
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Correlation between gene clusters
genomes RNASeqData
written 12 days ago by • 0
0
votes
2
replies
198
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
13 days ago • updated 11 days ago gingergeiger22 • 0
2
votes
1
reply
332
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 14 days ago by 43k • written 22 days ago by • 0
0
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1
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171
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 22 days ago by • 0 • written 25 days ago by • 0
1
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1
reply
276
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
0
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4
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655
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
12 weeks ago • updated 11 weeks ago Philippine • 0
0
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2
replies
374
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 12 weeks ago by • 0
3
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11
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811
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
1
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1
reply
402
views
WGCNA
DEGselection RNASeqData WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
1
vote
1
reply
280
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
1
vote
1
reply
491
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 4 months ago by 52k • written 4 months ago by • 0
1
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2
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1.3k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 4 months ago by • 0
1
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2
replies
357
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
4 months ago Gordon • 0
0
votes
3
replies
612
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
0
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4
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630
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
1
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3
replies
1.1k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
7 months ago Tanvi • 0
1
vote
3
replies
613
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
0
votes
1
reply
390
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
1
reply
393
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 4 months ago by ▴ 20 • written 8 months ago by • 0
0
votes
1
reply
414
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
votes
1
reply
352
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 9 months ago by 67k • written 9 months ago by • 0
3
votes
5
replies
1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
0
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0
replies
537
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 months ago Abril • 0
1
vote
2
replies
1.9k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 20 months ago by • 0
1
vote
3
replies
733
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 months ago island • 0
0
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2
replies
537
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
11 months ago Diana • 0
0
votes
1
reply
783
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
5
votes
6
replies
1.0k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
1
vote
1
reply
678
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
0
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2
replies
784
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago Luca • 0
0
votes
1
reply
1.1k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
1
vote
2
replies
806
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
13 months ago drewhaydensteele • 0
1
vote
1
reply
666
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
vote
2
replies
1.3k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
13 months ago • updated 12 months ago Levi • 0
0
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3
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1.7k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
13 months ago Oenone • 0
3
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4
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998
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
14 months ago pl23 • 0
0
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1
reply
564
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 14 months ago by 43k • written 14 months ago by ▴ 10
2
votes
2
replies
731
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
14 months ago Manthos • 0
0
votes
1
reply
668
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 14 months ago by ★ 13k • written 14 months ago by • 0
0
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2
replies
713
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
14 months ago Ben ▴ 10
0
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2
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1.8k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
14 months ago RHEA • 0
2
votes
3
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1.8k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
1
vote
1
reply
759
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 15 months ago by 67k • written 15 months ago by • 0
1
vote
7
replies
1.3k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 13 months ago by 52k • written 15 months ago by • 0
0
votes
1
reply
703
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 15 months ago by ▴ 780 • written 15 months ago by • 0
2
votes
4
replies
1.2k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
15 months ago Shihui • 0
0
votes
4
replies
1.1k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 16 months ago by 67k • written 16 months ago by ▴ 10
3
votes
3
replies
2.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
16 months ago Ethan Nguyen • 0
1
vote
1
reply
1.2k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 16 months ago by 67k • written 16 months ago by • 0
0
votes
2
replies
849
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
16 months ago Beyza • 0
50 results • Page 1 of 1
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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