Showing : RNA-Seq • reset
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 14 days ago by ▴ 990 • written 10 months ago by • 0
0
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1
reply
103
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First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 17 days ago by 44k • written 17 days ago by • 0
0
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1
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543
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create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 5 months ago by • 0 • written 19 months ago by • 0
0
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5
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211
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
5 months ago bioinformatic_trainee • 0
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0
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182
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
6 months ago lianov • 0
0
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1
reply
187
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
6 months ago • updated 5 months ago slcno • 0
1
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5
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409
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 7 months ago by 35k • written 7 months ago by ▴ 30
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1
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254
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 8 months ago by 3.4k • written 8 months ago by • 0
2
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3
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331
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 8 months ago by 44k • written 8 months ago by • 0
4
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2
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8.2k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 17 hours ago by • 0 • written 3.0 years ago by ▴ 20
1
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1
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309
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Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 8 months ago by ▴ 950 • written 8 months ago by ▴ 10
3
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4
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282
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need help regarding differential expression analysis
rna-seq
updated 8 months ago by 3.4k • written 8 months ago by ▴ 20
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0
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216
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
8 months ago rbrns • 0
1
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4
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1.6k
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 9 months ago by ▴ 950 • written 4.3 years ago by • 0
3
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4
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411
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Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
9 months ago Antonio M. • 0
1
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2
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350
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multifactorial design matrix
designmatrix RNA-seq limma
updated 10 months ago by 44k • written 10 months ago by ▴ 10
1
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7
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526
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how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
10 months ago decppced • 0
1
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3
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272
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Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 10 months ago by 35k • written 10 months ago by • 0
0
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0
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275
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
12 months ago wrzl • 0
3
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9
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753
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summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
13 months ago Pufall, Miles A ▴ 30
0
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1
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267
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Limma/Voom Normalized Counts
limma RNA-seq
updated 13 months ago by 44k • written 13 months ago by • 0
0
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2
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328
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 14 months ago by 44k • written 14 months ago by ▴ 60
0
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1
reply
286
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 14 months ago by 3.4k • written 15 months ago by • 0
2
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6
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626
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DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 11 months ago by 35k • written 15 months ago by • 0
0
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3
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449
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GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 15 months ago by ★ 2.8k • written 15 months ago by ▴ 60
0
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3
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343
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Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 15 months ago by 35k • written 15 months ago by • 0
0
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0
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462
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how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
15 months ago modarzi ▴ 10
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318
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Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
15 months ago mmartin ▴ 20
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239
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circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
15 months ago Terra • 0
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376
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HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
16 months ago ra711 • 0
3
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3
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461
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Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 16 months ago by 44k • written 16 months ago by ▴ 10
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3
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380
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Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
16 months ago microPhD • 0
5
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6
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582
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RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 16 months ago by 58k • written 16 months ago by ▴ 20
3
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1
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289
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How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 16 months ago by 58k • written 16 months ago by • 0
1
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1
reply
365
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Having issues mapping gene Ids during ReportingTools::publish() from Bioconductor.
ReportingTools RNA-Seq RMarkdown
updated 17 months ago by 58k • written 17 months ago by ▴ 20
0
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4
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369
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Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 17 months ago by 3.4k • written 17 months ago by ▴ 10
0
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1
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284
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dupRadar: low % of duplicates for 150bp PE RNAseq
dupRadar 150bp RNA-seq
updated 17 months ago by ▴ 70 • written 17 months ago by • 0
0
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4
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516
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Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 17 months ago by 35k • written 17 months ago by • 0
2
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1
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1.2k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 17 months ago by ★ 2.6k • written 17 months ago by ▴ 50
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330
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Job: Scientist 1, Bioinformatics (Research | Berkeley, CA | Full Time)
Bioinformatics drug-discovery RNA-seq CRISPR Job
17 months ago yzhang • 0
0
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0
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415
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Job: Postdoctoral Fellow in Sars-CoV-2 genomics and transcriptomics @ Paul-Ehrlich-Institute, Germany
rna-seq phylogenetics protein modelling single-cell sequencing Job
18 months ago liam.childs • 0
0
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1
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853
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
updated 18 months ago by ▴ 970 • written 18 months ago by ▴ 50
1
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2
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402
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DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 18 months ago by 35k • written 18 months ago by • 0
0
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2
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1.1k
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cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 19 months ago by ▴ 870 • written 19 months ago by ▴ 10
7
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6
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Odd DESeq2 results - high significance in genes with too many zeros
deseq2 rna-seq
updated 19 months ago by 35k • written 19 months ago by • 0
1
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2
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219
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EdgeR blocking factor - missing paired sample
EdgeR edgeR RNA-seq differential expression analysis blocking factors
updated 19 months ago by 44k • written 19 months ago by ▴ 30
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2
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558
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DESeq2 doubts about transformations + nbinomWaldtest warning
rna-seq deseq2 warnings nbinomWaldTest transformation
updated 19 months ago by 35k • written 19 months ago by • 0
0
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0
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229
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Pathview : why are some genes not colored?
pathview rna-seq
19 months ago okna0215 • 0
1
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0
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307
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Job: Bioinformatics Data Analyst
R RNA-seq job Job
19 months ago António Miguel de Jesus Domingues ▴ 480
1
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4
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308
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How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 19 months ago by 58k • written 19 months ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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