Showing : RNASeq • reset
1
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203
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 hours ago by 50k • written 1 day ago by • 0
0
votes
3
replies
204
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
0
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1
reply
164
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 20 days ago by 42k • written 21 days ago by • 0
0
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2
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185
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 22 days ago by • 0
0
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2
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234
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
26 days ago • updated 23 days ago catv • 0
0
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1
reply
123
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 27 days ago by 42k • written 27 days ago by • 0
5
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3
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299
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Log-cpm values from limma
limma edgeR RNASeq
updated 5 days ago by 50k • written 27 days ago by • 0
0
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1
reply
149
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
0
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2
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258
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 weeks ago • updated 7 weeks ago kcarey • 0
2
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2
replies
282
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
0
votes
2
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303
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago • updated 8 weeks ago kcarey • 0
1
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4
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321
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DESeq2 Replicates
DESeq2 RNASeq
9 weeks ago kcarey • 0
1
vote
3
replies
381
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by ▴ 10
0
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4
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319
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago • updated 10 weeks ago mperalc • 0
0
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2
replies
339
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
1
reply
274
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
3
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5
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657
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 11 weeks ago by ▴ 10
3
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6
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578
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
12 weeks ago boczniak767 ▴ 720
0
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0
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238
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
2
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2
replies
430
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
0
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4
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431
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
354
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
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3
replies
614
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
249
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
votes
4
replies
632
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
4
votes
6
replies
631
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
322
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
0
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3
replies
523
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
0
votes
1
reply
281
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
1
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2
replies
487
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
1
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2
replies
464
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
848
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
1
reply
385
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
2
votes
3
replies
508
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
0
votes
3
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476
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
replies
432
views
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 Manthos • 0
2
votes
4
replies
634
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
1
vote
4
replies
655
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
votes
0
replies
371
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
4
votes
2
replies
666
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
votes
6
replies
905
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
votes
2
replies
559
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 months ago by ★ 1.0k • written 6 months ago by ▴ 190
0
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1
reply
454
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
0
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0
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350
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
0
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2
replies
656
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
0
votes
0
replies
292
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
0
votes
0
replies
351
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
0
votes
0
replies
374
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
7 months ago Sara • 0
1
vote
1
reply
441
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
50 results • Page 1 of 1
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Marcel Ramos 690
`BiocManager` does not install local packages. It only installs Bioconductor, CRAN, and GitHub ones. You should install local packages w…
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Votes
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
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