Showing : rnaseq • reset
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95
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 days ago by ★ 4.0k • written 8 days ago by • 0
0
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5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 14 days ago by 50k • written 11.4 years ago by ▴ 30
0
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2
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686
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biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
4
votes
16
replies
7.2k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 26 days ago by • 0 • written 8.9 years ago by ▴ 150
0
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2
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189
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
27 days ago • updated 26 days ago kcarey • 0
0
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5
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9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 28 days ago by • 0 • written 7.6 years ago by • 0
0
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2
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219
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
4 weeks ago kcarey • 0
2
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2
replies
231
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
4 weeks ago Sabiha ▴ 20
0
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2
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1.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 5 weeks ago by • 0 • written 2.6 years ago by • 0
1
vote
4
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278
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DESeq2 Replicates
DESeq2 RNASeq
5 weeks ago kcarey • 0
1
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3
replies
320
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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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3
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426
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
3
votes
5
replies
583
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
0
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4
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259
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago • updated 6 weeks ago mperalc • 0
2
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5
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1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
0
votes
2
replies
247
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
1
reply
233
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
votes
6
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483
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
8 weeks ago • updated 7 weeks ago boczniak767 ▴ 720
0
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0
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186
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
8 weeks ago Abril • 0
4
votes
6
replies
531
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 9 weeks ago by 50k • written 3 months ago by • 0
2
votes
2
replies
353
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 weeks ago • updated 9 weeks ago jackafiore • 0
1
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2
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1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
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4
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354
views
Ballgown error in scan for c.tab files
ballgown RNASeq
10 weeks ago candacenewcome • 0
1
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3
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311
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 weeks ago • updated 10 weeks ago island • 0
1
vote
3
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536
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 11 weeks ago by • 0
0
votes
1
reply
213
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 12 weeks ago by ▴ 190 • written 12 weeks ago by • 0
2
votes
4
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516
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
12 weeks ago Sabiha ▴ 20
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
3
votes
1
reply
245
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
5
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7
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1.0k
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different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
0
votes
1
reply
245
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
3
votes
1
reply
1.6k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 3 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
3
replies
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
vote
2
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413
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
3 months ago Sabiha ▴ 20
5
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8
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3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 14 months ago by • 0
1
vote
8
replies
2.5k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
1
vote
7
replies
787
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
1
vote
2
replies
406
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
7
votes
2
replies
700
views
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
0
votes
3
replies
426
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
4 months ago Karthik • 0
2
votes
3
replies
434
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
4 months ago Karthik • 0
1
vote
1
reply
360
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
votes
2
replies
382
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
4 months ago Manthos • 0
2
votes
4
replies
578
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
414
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
0
votes
2
replies
507
views
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
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
1
vote
4
replies
587
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
50 results • Page 1 of 1
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Comment: DEG with low counts by Rajat • 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for your guide! I check my data as you said there is no difference in my data. This is the MDS plot at genes l…
Comment: How to correct for known and surrogate variables in DESeq2? by Michael Love 41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Votes
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
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