Showing : RNASeqData • reset
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227
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 18 days ago by 43k • written 25 days ago by • 0
0
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4
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624
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
8 weeks ago • updated 7 weeks ago Philippine • 0
0
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2
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349
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 8 weeks ago by • 0
3
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11
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762
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 weeks ago by • 0
1
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1
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341
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WGCNA
DEGselection RNASeqData WGCNA
updated 10 weeks ago by ▴ 760 • written 10 weeks ago by • 0
1
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1
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254
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
1
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1
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461
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 3 months ago by 52k • written 3 months ago by • 0
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2
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1.1k
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How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 3 months ago by • 0
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2
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333
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
3 months ago Gordon • 0
0
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3
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585
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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
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4
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594
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 5 months ago by • 0
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3
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968
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
6 months ago Tanvi • 0
1
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3
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574
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 months ago by 67k • written 6 months ago by ▴ 50
0
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1
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369
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
0
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1
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372
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 3 months ago by ▴ 20 • written 7 months ago by • 0
0
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1
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398
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
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1
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331
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 8 months ago by 67k • written 8 months ago by • 0
3
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5
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1.1k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 months ago by 43k • written 10 months ago by ▴ 10
0
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0
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515
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 months ago Abril • 0
1
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2
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1.8k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 19 months ago by • 0
1
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3
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704
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
10 months ago island • 0
0
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2
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522
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
10 months ago Diana • 0
0
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1
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744
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
5
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6
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995
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
11 months ago Shaimaa Gamal • 0
1
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1
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654
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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
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2
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744
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
12 months ago Luca • 0
0
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1
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1.0k
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 12 months ago by 67k • written 12 months ago by • 0
1
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2
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776
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
12 months ago drewhaydensteele • 0
1
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1
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646
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Differential gene expression analysis
RNASeqData RNAseq123
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
1
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2
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1.2k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
12 months ago Levi • 0
0
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3
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1.6k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
12 months ago Oenone • 0
3
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4
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966
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
13 months ago pl23 • 0
0
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1
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552
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 13 months ago by 43k • written 13 months ago by ▴ 10
2
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2
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708
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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
13 months ago Manthos • 0
0
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648
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 13 months ago by ★ 13k • written 13 months ago by • 0
0
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2
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694
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
13 months ago Ben ▴ 10
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2
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1.7k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
13 months ago RHEA • 0
2
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3
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1.7k
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
1
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1
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732
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Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 14 months ago by 67k • written 14 months ago by • 0
1
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7
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1.3k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 12 months ago by 52k • written 14 months ago by • 0
0
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1
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679
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
2
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4
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1.2k
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
15 months ago • updated 14 months ago Shihui • 0
0
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4
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1.0k
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 15 months ago by 67k • written 15 months ago by ▴ 10
3
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3
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2.4k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
15 months ago Ethan Nguyen • 0
1
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1
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1.2k
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 15 months ago by 67k • written 15 months ago by • 0
0
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2
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813
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
15 months ago Beyza • 0
1
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1
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732
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bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
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0
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507
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
15 months ago adi.rotem • 0
0
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1
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686
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
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1
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793
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Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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