Showing : RNASeqData • reset
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
3 days ago KR • 0
0
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1
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97
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 4 days ago by • 0 • written 6 days ago by • 0
1
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1
reply
241
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 27 days ago by 43k • written 4 weeks ago by • 0
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4
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635
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
9 weeks ago • updated 8 weeks ago Philippine • 0
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2
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359
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 9 weeks ago by • 0
3
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11
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784
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 weeks ago by • 0
1
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1
reply
360
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WGCNA
DEGselection RNASeqData WGCNA
updated 11 weeks ago by ▴ 760 • written 11 weeks ago by • 0
1
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1
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263
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
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1
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468
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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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343
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
4 months ago Gordon • 0
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3
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595
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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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608
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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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989
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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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589
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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
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1
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376
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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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379
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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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401
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
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1
reply
337
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 9 months ago by 67k • written 9 months ago by • 0
3
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5
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1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
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0
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519
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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 20 months ago by • 0
1
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3
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712
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 months ago island • 0
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2
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529
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
11 months ago Diana • 0
0
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1
reply
758
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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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1.0k
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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
reply
661
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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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758
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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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788
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
13 months ago drewhaydensteele • 0
1
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1
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651
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Differential gene expression analysis
RNASeqData RNAseq123
updated 13 months ago by ★ 4.6k • written 13 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
13 months ago • updated 12 months ago Levi • 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
13 months ago Oenone • 0
3
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4
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976
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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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553
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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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715
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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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1
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653
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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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698
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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
14 months ago • updated 13 months ago RHEA • 0
2
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3
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1.8k
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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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738
views
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 13 months ago by 52k • written 14 months ago by • 0
0
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1
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688
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 15 months ago by ▴ 780 • written 15 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 Shihui • 0
0
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4
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1.1k
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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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2.5k
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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
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2
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820
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
15 months ago Beyza • 0
1
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1
reply
736
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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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509
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
16 months ago • updated 15 months ago adi.rotem • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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