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2
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13
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467
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Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
24 days ago • updated 20 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
92
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
24 days ago
vaxahey107
• 0
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
0
votes
0
replies
103
views
I am trying to detect alternative splicing.
ASpli
25 days ago
Sebashish
• 0
3
votes
2
replies
226
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 23 days ago by
Guido Hooiveld
★ 4.0k • written 25 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
133
views
FDR via q-value
qvalue
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
John
• 0
0
votes
2
replies
234
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
26 days ago • updated 23 days ago
catv
• 0
0
votes
3
replies
169
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
bas_work
▴ 30
1
vote
0
replies
328
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
26 days ago
BioinfGuru
▴ 30
0
votes
2
replies
144
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
26 days ago
prity6459
• 0
2
votes
2
replies
207
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
sansan
• 0
0
votes
4
replies
213
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
27 days ago • updated 26 days ago
sropri
• 0
2
votes
4
replies
270
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 23 days ago by
James W. MacDonald
65k • written 27 days ago by
Mirella Aurora
• 0
0
votes
3
replies
207
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 27 days ago by
prity6459
• 0
0
votes
0
replies
130
views
Warning while loading DEP package
DEP
updated 27 days ago by
shepherl
3.9k • written 27 days ago by
Namrata
• 0
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
0
votes
1
reply
151
views
rlog transformation
DESeq2
updated 27 days ago by
Michael Love
42k • written 27 days ago by
ishij9717
• 0
0
votes
1
reply
123
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 27 days ago by
Michael Love
42k • written 27 days ago by
09191919
• 0
5
votes
3
replies
298
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 27 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
232
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
27 days ago • updated 26 days ago
Le
• 0
1
vote
2
replies
174
views
Error in champ.load(): The following specified files do not exist
ChAMP
27 days ago
Sherin
• 0
0
votes
1
reply
105
views
Input Question for deseq.r
RSeqAn
updated 27 days ago by
ATpoint
★ 4.1k • written 28 days ago by
Nina
• 0
4
votes
6
replies
457
views
FilterByExpr low counts with small sample size
edgeR
28 days ago • updated 23 days ago
Jonathan
▴ 10
0
votes
4
replies
257
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
28 days ago • updated 25 days ago
lonn
• 0
1
vote
2
replies
732
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
28 days ago • updated 19 days ago
Patadù
▴ 10
0
votes
1
reply
162
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 27 days ago by
ATpoint
★ 4.1k • written 28 days ago by
quanah.hudson
• 0
0
votes
7
replies
347
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
28 days ago • updated 22 days ago
hortense96
• 0
0
votes
0
replies
91
views
News:
Services
flowBeads
28 days ago
creativepeptides2018
• 0
0
votes
0
replies
89
views
Enzyme Engineering
BioTIP
28 days ago
bocchemistry
• 0
0
votes
0
replies
90
views
News:
TIDES USA 2024
flowBeads
28 days ago
bocsci11
• 0
0
votes
1
reply
143
views
covariate with negative and positive values
DESeq2
updated 27 days ago by
Michael Love
42k • written 28 days ago by
Brynn
• 0
0
votes
1
reply
163
views
Adding columns to DEXSeqResults object
DEXSeq
updated 27 days ago by
Alejandro Reyes
★ 1.9k • written 29 days ago by
Clyde
• 0
0
votes
0
replies
102
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
29 days ago • updated 28 days ago
Maliha Tabassum
• 0
1
vote
2
replies
161
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
29 days ago
Ana
• 0
0
votes
1
reply
128
views
what is the sampleFiles
chipseq
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
zhulin
• 0
0
votes
4
replies
210
views
flowStats Search Error
flowStats
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
tholmes
• 0
0
votes
0
replies
103
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
29 days ago
Virangika
• 0
0
votes
3
replies
221
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
andrebolerbarros
▴ 20
2
votes
3
replies
340
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 weeks ago • updated 29 days ago
daniel.carbajo
• 0
0
votes
4
replies
289
views
DEG with low counts
DESeq2
updated 26 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
1
vote
1
reply
202
views
Differentially expressed genes in monocle pseudotime
monocle
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
kthapa
• 0
0
votes
1
reply
150
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
tian.liu0720
• 0
2
votes
2
replies
183
views
[DiffBind] Obtaining normalization factors
DiffBind
4 weeks ago • updated 29 days ago
Henry
▴ 10
3
votes
3
replies
237
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
4 weeks ago • updated 27 days ago
jacques.imbert
• 0
0
votes
3
replies
274
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 27 days ago by
W. Evan Johnson
▴ 850 • written 4 weeks ago by
schlumbohm
• 0
4
votes
9
replies
477
views
Memory errors using read.bismark?
dmrseq
bsseq
4 weeks ago • updated 8 days ago
Juan Higareda
• 0
0
votes
1
reply
161
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 29 days ago by
kamryncole1963
• 0 • written 4 weeks ago by
Sara
• 0
1
vote
2
replies
257
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 26 days ago
Weiqian
▴ 10
5
votes
9
replies
964
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
4 weeks ago • updated 27 days ago
Chris
▴ 10
3
votes
3
replies
362
views
permutation test in edgeR
rna-seq
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
197 results • Page
3 of 4
Recent ...
Replies
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…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Guido Hooiveld
★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
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
Answer: How to design DEXSeq formula for multiple variables
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