Showing : rnaseqdata • reset
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 12 weeks ago by • 0
0
votes
2
replies
577
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 10 weeks ago by • 0 • written 4 months ago by • 0
3
votes
13
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2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
0
votes
1
reply
832
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
vote
1
reply
505
views
Merging annotation with differential expression output
annotation RNASeqData
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
3
replies
1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
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415
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
12 months ago cftattersfield • 0
0
votes
5
replies
828
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
0
votes
1
reply
540
views
Correlation between gene clusters
genomes RNASeqData
written 13 months ago by • 0
0
votes
2
replies
843
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
13 months ago gingergeiger22 • 0
2
votes
1
reply
801
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
1
reply
759
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 13 months ago by • 0 • written 13 months ago by • 0
2
votes
1
reply
924
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
4
replies
1.3k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
15 months ago Philippine • 0
0
votes
2
replies
1.1k
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 15 months ago by • 0
1
vote
1
reply
1.0k
views
WGCNA
DEGselection RNASeqData WGCNA
updated 16 months ago by ▴ 760 • written 16 months ago by • 0
1
vote
1
reply
771
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
1
vote
1
reply
984
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 17 months ago by 53k • written 17 months ago by • 0
1
vote
2
replies
4.0k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 17 months ago by • 0
1
vote
2
replies
852
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
17 months ago Gordon • 0
0
votes
3
replies
1.1k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
4
replies
1.2k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 19 months ago by • 0
1
vote
3
replies
2.1k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
20 months ago Tanvi • 0
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 20 months ago by 68k • written 20 months ago by ▴ 50
0
votes
1
reply
719
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
1
reply
807
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 17 months ago by ▴ 20 • written 21 months ago by • 0
0
votes
1
reply
692
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
1
reply
744
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 22 months ago by 68k • written 22 months ago by • 0
3
votes
5
replies
1.9k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 23 months ago by 43k • written 24 months ago by ▴ 10
0
votes
0
replies
834
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
24 months ago Abril • 0
1
vote
2
replies
2.6k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.8 years ago by • 0
1
vote
3
replies
1.3k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
2.0 years ago island • 0
0
votes
2
replies
888
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
2.0 years ago Diana • 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
5
votes
6
replies
1.7k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
2.1 years ago Shaimaa Gamal • 0
1
vote
1
reply
1.0k
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
votes
2
replies
1.9k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
2.2 years ago Luca • 0
0
votes
1
reply
1.9k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
2
replies
1.3k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.2 years ago drewhaydensteele • 0
1
vote
1
reply
1.0k
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
1
vote
2
replies
2.1k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.2 years ago • updated 2.1 years ago Levi • 0
0
votes
3
replies
2.8k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
2.2 years ago Oenone • 0
3
votes
4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.2 years ago pl23 • 0
0
votes
1
reply
834
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
2
votes
2
replies
1.2k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.2 years ago Manthos • 0
0
votes
1
reply
962
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.2 years ago by ★ 13k • written 2.3 years ago by • 0
0
votes
2
replies
1.1k
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.3 years ago Ben ▴ 10
0
votes
2
replies
3.0k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
2.3 years ago RHEA • 0
2
votes
3
replies
2.9k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
152 results • Page 1 of 4
Recent ...
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Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Erik Wright ▴ 150
This has to do with the fact that some taxonomies reuse names at the same rank level. Common examples in the SILVA taxonomy are "Incertae S…
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Votes
Answer: Can you colour dendrogram branch clusters in pheatmap?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
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