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Showing :
RNAseq
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0
votes
1
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25
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
written 3 hours ago by
kcarey
• 0
1
vote
3
replies
809
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 10 hours ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
83
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
taur.vil
• 0
0
votes
2
replies
147
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 days ago • updated 2 days ago
catv
• 0
0
votes
1
reply
107
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
85
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
0
votes
2
replies
884
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 7 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
1
reply
119
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 14 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Merav
• 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 22 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
0
votes
2
replies
690
views
biomart not ound some prevous release
biomart
rnaseq
written 5.2 years ago by
jarod_v6@libero.it
▴ 40
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 4 weeks ago by
Shaimaa Gamal
• 0 • written 8.9 years ago by
Pauly Lin
▴ 150
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
5 weeks ago • updated 4 weeks ago
kcarey
• 0
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 5 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
0
votes
2
replies
236
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
6 weeks ago • updated 5 weeks ago
kcarey
• 0
2
votes
2
replies
243
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 weeks ago
Sabiha
▴ 20
0
votes
2
replies
1.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 6 weeks ago by
leedakyung1998
• 0 • written 2.7 years ago by
MP
• 0
1
vote
4
replies
290
views
DESeq2 Replicates
DESeq2
RNASeq
6 weeks ago
kcarey
• 0
1
vote
3
replies
338
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 7 weeks ago by
swbarnes2
★ 1.3k • written 7 weeks ago by
sap275
▴ 10
0
votes
3
replies
453
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 3 months ago by
Fayrouz
• 0
3
votes
5
replies
599
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 7 weeks ago by
Michael Love
41k • written 8 weeks ago by
sap275
▴ 10
0
votes
4
replies
272
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
8 weeks ago • updated 7 weeks ago
mperalc
• 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 0
0
votes
2
replies
259
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
ryann
• 0
2
votes
1
reply
243
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 8 weeks ago by
Michael Love
41k • written 8 weeks ago by
sap275
▴ 10
3
votes
6
replies
502
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
9 weeks ago
boczniak767
▴ 720
0
votes
0
replies
201
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
9 weeks ago
Abril
• 0
4
votes
6
replies
554
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 10 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
375
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
11 weeks ago
jackafiore
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 11 months ago by
informatician
• 0
0
votes
4
replies
371
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
12 weeks ago • updated 11 weeks ago
candacenewcome
• 0
1
vote
3
replies
319
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
12 weeks ago
island
• 0
1
vote
3
replies
552
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
219
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
542
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 3 months ago by
Shaimaa Gamal
• 0 • written 7.1 years ago by
myprogramming2016
• 0
3
votes
1
reply
263
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
5
votes
7
replies
1.0k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 3 months ago by
Gordon Smyth
50k • written 13 months ago by
Ilya
• 0
0
votes
1
reply
254
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
3 months ago
WS
• 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR
RnaSeqSampleSizeData
RNAseq
updated 3 months ago by
Gordon Smyth
50k • written 3.0 years ago by
Lucy
▴ 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 4 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
1
vote
2
replies
430
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.1 years ago by
panagiotis.mokos
▴ 40
0
votes
2
replies
1.3k
views
Conducting pair-wise comparison in DESeq2?
DESeq2
deseq2
biocondu
Bioconductor
RNASeq
written 14 months ago by
Hussain
• 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
Jon
• 0 • written 3.3 years ago by
Archit
▴ 10
1
vote
7
replies
809
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 6 months ago by
Gimena
• 0
1
vote
2
replies
419
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
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
7
votes
2
replies
761
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
0
votes
3
replies
439
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago • updated 4 months ago
Karthik
• 0
2
votes
3
replies
450
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
5 months ago • updated 4 months ago
Karthik
• 0
50 results • Page
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Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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