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0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
22 days ago • updated 21 days ago
kcarey
• 0
2
votes
1
reply
152
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 17 days ago by
Michael Love
42k • written 17 days ago by
mat149
▴ 70
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 23 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
5
replies
243
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 17 hours ago by
xuz
• 0 • written 2 days ago by
minardsmitha
▴ 10
3
votes
4
replies
279
views
Help with error using camera() in limma
CAMERA
limma
23 days ago
Chris
▴ 10
0
votes
2
replies
145
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
7 days ago
makala
• 0
0
votes
3
replies
197
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 23 days ago by
Alejandro Reyes
★ 1.9k • written 5 weeks ago by
Alessia
• 0
0
votes
8
replies
561
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 9 days ago by
BioinfGuru
▴ 30 • written 10 days ago by
Eric Katagirya
• 0
4
votes
11
replies
1.6k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData
genomeinfodbdata
updated 1 day ago by
merv
▴ 120 • written 9 months ago by
15753563659
▴ 60
0
votes
3
replies
103
views
pathview error
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 4.0k • written 2 days ago by
Fara
• 0
0
votes
1
reply
170
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
kcarey
• 0
4
votes
2
replies
650
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
21 days ago • updated 17 days ago
gene_bioconductor
▴ 10
0
votes
4
replies
388
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 12 days ago by
Ziliang
• 0 • written 23 days ago by
Ian D.
▴ 70
0
votes
2
replies
760
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 8 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 23 days ago
Chris
▴ 10
1
vote
5
replies
533
views
Can't post a question containing code?
Bioconductor
updated 13 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
2
votes
2
replies
426
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
12 days ago • updated 7 days ago
Matthew Thornton
▴ 360
4
votes
3
replies
146
views
recount3 problem downloading data from source sra
recount3
updated 1 day ago by
Leonardo Collado Torres
★ 1.1k • written 2 days ago by
PABLO ANTONIO
▴ 10
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 17 days ago by
Caio
• 0 • written 13.2 years ago by
boczniak767
▴ 720
0
votes
2
replies
57
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 9 hours ago by
Michael Love
42k • written 10 hours ago by
tjl
• 0
2
votes
9
replies
449
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 28 days ago by
James W. MacDonald
66k • written 28 days ago by
Alexandre
• 0
0
votes
4
replies
271
views
Minfi - estimatecellscount
min
minfi
updated 24 days ago by
James W. MacDonald
66k • written 7 weeks ago by
clacarion
• 0
0
votes
1
reply
83
views
ERROR; return code from pthread_create() is 22
affy
updated 3 days ago by
James W. MacDonald
66k • written 5 days ago by
pickingastar
• 0
1
vote
1
reply
185
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 3 days ago by
James W. MacDonald
66k • written 4 days ago by
ttt
• 0
3
votes
7
replies
907
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
3
votes
3
replies
279
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 25 days ago by
ATpoint
★ 4.2k • written 25 days ago by
bioinf
▴ 10
0
votes
5
replies
183
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
5 days ago • updated 3 days ago
Galina
• 0
1
vote
2
replies
222
views
Improving the design matrices vignette in RNAseq123
RNAseq123
4 weeks ago • updated 17 days ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
144
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
Agung
• 0
1
vote
3
replies
261
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 27 days ago by
Michael Love
42k • written 28 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
183
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 21 days ago by
Gordon Smyth
50k • written 21 days ago by
z_bahari
• 0
1
vote
2
replies
406
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
7 weeks ago • updated 20 days ago
Kim
• 0
0
votes
6
replies
599
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
6 days ago • updated 3 days ago
Ken C
• 0
1
vote
4
replies
366
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 weeks ago • updated 28 days ago
winwater0928
• 0
1
vote
2
replies
138
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
9 days ago • updated 8 days ago
Patadù
▴ 10
0
votes
3
replies
310
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
HAK
• 0
2
votes
4
replies
1.8k
views
slingshot: error with plot3d.SlingshotDataSet
slingshot
plot3d.SlingshotDataSet
updated 1 day ago by
Kelly Street
• 0 • written 23 months ago by
manduchi
▴ 10
3
votes
5
replies
317
views
Help with running egsea()
EGSEA
17 days ago • updated 16 days ago
Chris
▴ 10
0
votes
2
replies
968
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 8 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
5
votes
3
replies
328
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 14 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Shaimaa Gamal
• 0
0
votes
2
replies
179
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
24 days ago • updated 21 days ago
Aurora
• 0
2
votes
2
replies
297
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
16 days ago • updated 11 days ago
zzrammal
• 0
1
vote
4
replies
537
views
DEseq2 coefficient
DESeq2
coefficient
3 months ago • updated 22 days ago
JKim
• 0
0
votes
1
reply
184
views
ATACseq merge peaks
DiffBind
updated 27 days ago by
ATpoint
★ 4.2k • written 29 days ago by
Shloka
• 0
1
vote
5
replies
1.6k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 16 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
4
votes
9
replies
318
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 7 days ago by
ATpoint
★ 4.2k • written 9 days ago by
pangtaihin
• 0
0
votes
2
replies
201
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 4 weeks ago by
taur.vil
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 8 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
1
vote
1
reply
199
views
Handling multiple differential expression comparisons
DESeq2
updated 18 days ago by
Michael Love
42k • written 20 days ago by
Zainab
▴ 10
2
votes
3
replies
173
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
Guillermo
• 0
182 results • Page
2 of 4
Recent ...
Replies
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
Wei Shi
★ 3.6k
Your bam file names should be stored in a vector and then provided to the `files` parameter.
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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★ 4.2k
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