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RNAseq
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0
votes
0
replies
11
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
2 hours ago • updated 1 hour ago
james.zhang20
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 22 hours ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
123
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
0
votes
1
reply
129
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
taur.vil
• 0
0
votes
2
replies
192
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
12 days ago • updated 9 days ago
catv
• 0
3
votes
1
reply
155
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
100
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 13 days ago by
Michael Love
41k • written 13 days ago by
09191919
• 0
0
votes
1
reply
132
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Merav
• 0
0
votes
2
replies
225
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
6 weeks ago • updated 5 weeks ago
kcarey
• 0
2
votes
2
replies
255
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
6 weeks ago
Sabiha
▴ 20
0
votes
2
replies
258
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
7 weeks ago • updated 6 weeks ago
kcarey
• 0
1
vote
4
replies
301
views
DESeq2 Replicates
DESeq2
RNASeq
8 weeks ago
kcarey
• 0
1
vote
3
replies
355
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 8 weeks ago by
swbarnes2
★ 1.3k • written 8 weeks ago by
sap275
▴ 10
0
votes
4
replies
293
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
9 weeks ago • updated 8 weeks ago
mperalc
• 0
0
votes
2
replies
288
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
ryann
• 0
3
votes
5
replies
615
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 8 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
2
votes
1
reply
258
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 9 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
3
votes
6
replies
522
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
10 weeks ago
boczniak767
▴ 720
0
votes
0
replies
218
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
10 weeks ago
Abril
• 0
2
votes
2
replies
401
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
12 weeks ago
jackafiore
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
0
votes
4
replies
390
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
3 months ago
candacenewcome
• 0
1
vote
3
replies
332
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
3 months ago
island
• 0
1
vote
3
replies
565
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 3 months ago by
georgii.vdovin
• 0
0
votes
1
reply
230
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 3 months ago by
Ram
▴ 190 • written 3 months ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
576
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
580
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 12 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
288
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
475
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 3 months ago by
Fayrouz
• 0
0
votes
1
reply
265
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
3 months ago
WS
• 0
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
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
1
vote
2
replies
451
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
1
vote
2
replies
437
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
5 months ago • updated 4 months ago
drewhaydensteele
• 0
7
votes
2
replies
792
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
3
replies
452
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
1
vote
1
reply
373
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 5 months ago by
Michael Love
41k • written 5 months ago by
pl23
• 0
2
votes
3
replies
467
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
5 months ago
Karthik
• 0
2
votes
2
replies
401
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
601
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
5 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
433
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 5 months ago by
Michael Love
41k • written 6 months ago by
Sean
• 0
0
votes
2
replies
530
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 5 months ago by
Leonardo Collado Torres
★ 1.0k • written 6 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 5 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
1
vote
4
replies
621
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
351
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
617
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
839
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
334
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
6 months ago
Sara
• 0
0
votes
2
replies
635
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
6 months ago
Karthik
• 0
0
votes
0
replies
276
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
0
votes
0
replies
334
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
6 months ago
Xinqi
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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