Showing : RNAseq • reset
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 hours ago by 41k • written 1 day ago by • 0
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56
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Log-cpm values from limma
limma edgeR RNASeq
updated 4 hours ago by 50k • written 1 day ago by • 0
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1
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106
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 days ago by ★ 4.0k • written 10 days ago by • 0
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2
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198
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
29 days ago • updated 28 days ago kcarey • 0
2
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2
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238
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
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2
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226
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
1
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4
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281
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
1
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3
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329
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
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4
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262
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago mperalc • 0
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2
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249
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
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1
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237
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
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5
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585
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
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6
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489
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Average biological replicates in RNA-seq
Mfuzz RNASeq
8 weeks ago boczniak767 ▴ 720
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191
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
2
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2
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362
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 weeks ago jackafiore • 0
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4
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359
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Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago candacenewcome • 0
1
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3
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315
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 weeks ago island • 0
1
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3
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541
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 12 weeks ago by • 0
0
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1
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215
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 12 weeks ago by ▴ 190 • written 12 weeks ago by • 0
2
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4
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522
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
12 weeks ago Sabiha ▴ 20
4
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6
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539
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
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1
reply
248
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
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3
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438
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
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1
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249
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
1
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2
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420
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago • updated 3 months ago Sabiha ▴ 20
2
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3
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1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 3 months ago by ★ 1.3k • written 4 months ago by • 0
1
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2
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413
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
7
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2
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728
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
1
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1
reply
361
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
2
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3
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441
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
4 months ago Karthik • 0
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3
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430
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
4 months ago Karthik • 0
2
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2
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384
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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
5 months ago • updated 4 months ago Manthos • 0
2
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4
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580
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limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
1
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4
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593
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
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0
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336
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
4
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2
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571
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
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6
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793
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
5 months ago erika.maldonado-rosado • 0
0
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2
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508
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 5 months ago by ▴ 190
0
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1
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415
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 5 months ago by 41k • written 6 months ago by • 0
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0
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318
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
0
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2
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617
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
0
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0
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257
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
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0
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319
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
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0
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315
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
1
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1
reply
394
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
1
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7
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797
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
0
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2
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401
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Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 6 months ago by ★ 1.3k • written 6 months ago by • 0
0
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1
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384
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 6 months ago by ▴ 770 • written 6 months ago by • 0
3
votes
5
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797
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
1
vote
1
reply
434
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
50 results • Page 1 of 1
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Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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