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4
votes
9
replies
477
views
Memory errors using read.bismark?
dmrseq
bsseq
4 weeks ago • updated 8 days ago
Juan Higareda
• 0
2
votes
1
reply
144
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
e1271094
• 0
0
votes
1
reply
94
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 8 days ago by
shepherl
3.9k • written 8 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
74
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
8 days ago
Dinesh
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 9 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
203
views
Couldn't connect to server while using "pathways"
graphite
updated 9 days ago by
Michael Love
42k • written 9 days ago by
fduguchunhui
• 0
4
votes
2
replies
613
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
13 days ago • updated 9 days ago
gene_bioconductor
▴ 10
3
votes
1
reply
135
views
How to save the DEXSeq results
DEXSeq
updated 9 days ago by
Michael Love
42k • written 9 days ago by
Sara
• 0
2
votes
1
reply
126
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 9 days ago by
Michael Love
42k • written 9 days ago by
mat149
▴ 70
1
vote
2
replies
209
views
Improving the design matrices vignette in RNAseq123
RNAseq123
23 days ago • updated 9 days ago
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
252
views
package goseq seems to be not available on the latest version of R
goseq
updated 9 days ago by
Gordon Smyth
50k • written 11 days ago by
Patrycja
▴ 20
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 9 days ago
Henrik Bengtsson
★ 2.4k
2
votes
2
replies
214
views
fgsea significant result
fgsea
10 days ago
Chris
▴ 10
1
vote
1
reply
176
views
Handling multiple differential expression comparisons
DESeq2
updated 10 days ago by
Michael Love
42k • written 12 days ago by
Zainab
▴ 10
2
votes
3
replies
243
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 10 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Reza
• 0
0
votes
6
replies
276
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 11 days ago by
swbarnes2
★ 1.4k • written 12 days ago by
arfranco
▴ 130
1
vote
2
replies
388
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 11 days ago by
Gordon Smyth
50k • written 11 days ago by
Kim
• 0
0
votes
0
replies
129
views
Empty table plot using plotGseaTable()
fgsea
14 days ago • updated 11 days ago
Chris
▴ 10
1
vote
2
replies
355
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 11 days ago
Kim
• 0
0
votes
0
replies
111
views
dba.plotProfile() plotting and interpretation
DiffBind
12 days ago
Henry
▴ 10
0
votes
2
replies
161
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
15 days ago • updated 12 days ago
Aurora
• 0
0
votes
0
replies
139
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
20 days ago • updated 12 days ago
glaciya2018
• 0
0
votes
2
replies
201
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
13 days ago • updated 12 days ago
kcarey
• 0
0
votes
1
reply
169
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
z_bahari
• 0
0
votes
1
reply
151
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
c53aba27
• 0
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
13 days ago
tholmes
• 0
0
votes
2
replies
156
views
DESeq2 v1.35.0
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 13 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
13 days ago
yvonneh
• 0
0
votes
0
replies
79
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
13 days ago
Ian D.
▴ 70
0
votes
1
reply
124
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 13 days ago by
4r-rtg
• 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
ATpoint
★ 4.1k • written 13 days ago by
james.zhang20
• 0
0
votes
2
replies
185
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 22 days ago by
taur.vil
• 0
1
vote
2
replies
279
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
14 days ago • updated 13 days ago
Yveto
• 0
0
votes
3
replies
293
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 13 days ago by
Michael Love
42k • written 14 days ago by
HAK
• 0
4
votes
0
replies
125
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
13 days ago
shepherl
3.9k
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
25 days ago • updated 14 days ago
Chris
▴ 10
1
vote
4
replies
507
views
DEseq2 coefficient
DESeq2
coefficient
11 weeks ago • updated 14 days ago
JKim
• 0
3
votes
4
replies
256
views
Help with error using camera() in limma
CAMERA
limma
15 days ago • updated 14 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 15 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 15 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
259
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
SSSJec
• 0
0
votes
3
replies
269
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
SSSJec
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 15 days ago
Chris
▴ 10
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 15 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
179
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 15 days ago by
Alejandro Reyes
★ 1.9k • written 27 days ago by
Alessia
• 0
1
vote
1
reply
146
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
marcusn
• 0
0
votes
1
reply
135
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Agung
• 0
0
votes
0
replies
91
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
15 days ago
Maria Doyle
▴ 70
0
votes
1
reply
117
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 15 days ago by
shepherl
3.9k • written 15 days ago by
bounlu
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
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`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
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
Answer: SGSeq: moving toward diffex from SGSeq analysis
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