Showing : RNASeqData • reset
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 5 days ago by 66k • written 5 days ago by ▴ 50
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1
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125
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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 10 days ago by 66k • written 10 days ago by • 0
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0
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107
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
4 weeks ago Shaimaa Gamal • 0
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1
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206
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 6 weeks ago by 51k • written 6 weeks ago by • 0
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1
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146
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 10 weeks ago by 66k • written 10 weeks ago by • 0
3
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5
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722
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
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294
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
4 months ago Abril • 0
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2
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1.3k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 13 months ago by • 0
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3
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408
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
4 months ago island • 0
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2
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321
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
4 months ago Diana • 0
0
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1
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397
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
5
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6
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652
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago Shaimaa Gamal • 0
1
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1
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441
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
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2
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415
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
6 months ago Luca • 0
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1
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407
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 6 months ago by 66k • written 6 months ago by • 0
1
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2
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507
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
6 months ago drewhaydensteele • 0
1
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1
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384
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Differential gene expression analysis
RNASeqData RNAseq123
updated 6 months ago by ★ 4.2k • written 6 months ago by • 0
1
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2
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769
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
6 months ago • updated 5 months ago Levi • 0
0
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3
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808
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
6 months ago Oenone • 0
3
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4
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601
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
6 months ago pl23 • 0
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1
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405
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 6 months ago by 42k • written 7 months ago by ▴ 10
2
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2
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474
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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
6 months ago Manthos • 0
0
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1
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456
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 7 months ago by ★ 13k • written 7 months ago by • 0
0
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2
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492
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
7 months ago Ben • 0
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817
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MA plot for DESEq2 analysis
RNASeqData DESeq2
7 months ago RHEA • 0
2
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3
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943
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
1
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1
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476
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Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 8 months ago by 66k • written 8 months ago by • 0
1
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7
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929
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 6 months ago by 51k • written 8 months ago by • 0
0
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1
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449
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 8 months ago by ▴ 780 • written 8 months ago by • 0
2
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4
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787
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
8 months ago Shihui • 0
0
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4
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728
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 8 months ago by 66k • written 8 months ago by ▴ 10
3
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3
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1.4k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
9 months ago Ethan Nguyen • 0
0
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1
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730
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 9 months ago by 66k • written 9 months ago by • 0
0
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2
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576
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
9 months ago Beyza • 0
1
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1
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503
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bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 9 months ago by ★ 4.2k • written 9 months ago by • 0
0
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0
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358
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
9 months ago adi.rotem • 0
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1
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531
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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 9 months ago by ★ 4.2k • written 9 months ago by • 0
0
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1
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560
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Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
2
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3
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1.3k
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 10 months ago by 66k • written 10 months ago by ▴ 10
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2
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1.1k
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 10 months ago by 66k • written 10 months ago by • 0
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2
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1.1k
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
10 months ago Marina • 0
1
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2
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1.7k
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 10 months ago by ▴ 120 • written 10 months ago by ▴ 10
0
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6
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841
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 51k • written 10 months ago by • 0
1
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2
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575
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I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 10 months ago by 42k • written 11 months ago by • 0
0
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0
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362
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
11 months ago sonal • 0
1
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9
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936
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DESeq2 not replicable results
RNASeqData DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
0
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0
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592
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
11 months ago info ▴ 10
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1
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572
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DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
1
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1
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484
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 11 months ago by 51k • written 11 months ago by • 0
2
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1
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780
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Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 11 months ago by 66k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: biomaRt not working - lazy table error
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
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