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1
vote
13
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363
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Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
9 days ago • updated 6 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
73
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
10 days ago
vaxahey107
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
11 days ago • updated 14 hours ago
Chris
• 0
0
votes
0
replies
89
views
I am trying to detect alternative splicing.
ASpli
11 days ago
Sebashish
• 0
3
votes
2
replies
196
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 9 days ago by
Guido Hooiveld
★ 3.9k • written 11 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
132
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
bas_work
▴ 30
2
votes
2
replies
171
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
sansan
• 0
1
vote
0
replies
245
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
12 days ago • updated 11 days ago
BioinfGuru
▴ 30
4
votes
6
replies
390
views
FilterByExpr low counts with small sample size
edgeR
14 days ago • updated 9 days ago
Jonathan
▴ 10
0
votes
2
replies
116
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
12 days ago
prity6459
• 0
0
votes
3
replies
165
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 12 days ago by
Gordon Smyth
50k • written 12 days ago by
prity6459
• 0
3
votes
1
reply
154
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
4
replies
170
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
12 days ago
sropri
• 0
0
votes
3
replies
148
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 13 days ago by
Alessia
• 0
0
votes
1
reply
142
views
Adding columns to DEXSeqResults object
DEXSeq
updated 13 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Clyde
• 0
0
votes
0
replies
108
views
Warning while loading DEP package
DEP
updated 13 days ago by
shepherl
3.8k • written 13 days ago by
Namrata
• 0
0
votes
1
reply
117
views
rlog transformation
DESeq2
updated 13 days ago by
Michael Love
41k • written 13 days ago by
ishij9717
• 0
0
votes
1
reply
99
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
1
vote
2
replies
687
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
0
votes
1
reply
120
views
covariate with negative and positive values
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
Brynn
• 0
0
votes
1
reply
135
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
quanah.hudson
• 0
1
vote
2
replies
202
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
13 days ago • updated 12 days ago
Le
• 0
1
vote
2
replies
143
views
Error in champ.load(): The following specified files do not exist
ChAMP
13 days ago
Sherin
• 0
0
votes
1
reply
92
views
Input Question for deseq.r
RSeqAn
updated 13 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Nina
• 0
0
votes
4
replies
218
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 days ago • updated 11 days ago
lonn
• 0
0
votes
7
replies
284
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
14 days ago • updated 8 days ago
hortense96
• 0
0
votes
0
replies
69
views
News:
Services
flowBeads
14 days ago
creativepeptides2018
• 0
0
votes
0
replies
73
views
Enzyme Engineering
BioTIP
14 days ago
bocchemistry
• 0
0
votes
0
replies
70
views
News:
TIDES USA 2024
flowBeads
14 days ago
bocsci11
• 0
0
votes
0
replies
85
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
14 days ago
Maliha Tabassum
• 0
0
votes
4
replies
174
views
flowStats Search Error
flowStats
updated 14 days ago by
shepherl
3.8k • written 15 days ago by
tholmes
• 0
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 13 days ago
shepherl
3.8k
0
votes
1
reply
132
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 15 days ago by
James W. MacDonald
65k • written 17 days ago by
tian.liu0720
• 0
1
vote
2
replies
127
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
15 days ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
111
views
what is the sampleFiles
chipseq
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
zhulin
• 0
1
vote
1
reply
175
views
Differentially expressed genes in monocle pseudotime
monocle
updated 15 days ago by
Gordon Smyth
50k • written 17 days ago by
kthapa
• 0
4
votes
8
replies
380
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 12 days ago by
Peter Hickey
▴ 740 • written 20 days ago by
Juan Higareda
• 0
3
votes
3
replies
190
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
19 days ago • updated 13 days ago
jacques.imbert
• 0
0
votes
1
reply
133
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 15 days ago by
kamryncole1963
• 0 • written 20 days ago by
Sara
• 0
0
votes
3
replies
192
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
87
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
15 days ago
Virangika
• 0
0
votes
0
replies
65
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
16 days ago
Henry
▴ 10
1
vote
2
replies
235
views
How to retrieve detailed regression results from deseq2
DESeq2
20 days ago • updated 11 days ago
Weiqian
▴ 10
0
votes
4
replies
252
views
DEG with low counts
DESeq2
updated 12 days ago by
Michael Love
41k • written 16 days ago by
Rajat
• 0
1
vote
2
replies
464
views
GSVA error
GSVA
17 days ago • updated 16 days ago
Alex
• 0
2
votes
3
replies
311
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
16 days ago • updated 15 days ago
daniel.carbajo
• 0
3
votes
3
replies
310
views
permutation test in edgeR
rna-seq
edgeR
updated 10 days ago by
Gordon Smyth
50k • written 23 days ago by
Netanel
• 0
1
vote
3
replies
338
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 16 days ago by
Gordon Smyth
50k • written 21 days ago by
Simran
• 0
0
votes
1
reply
121
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Sahar
• 0
45,597 results • Page
2 of 912
Recent ...
Replies
Answer: Store output of matchPWM()
by
James W. MacDonald
65k
Something like this? ``` ind <- as.logical(sapply(hitlist, length)) out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) …
Answer: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
James W. MacDonald
65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Votes
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
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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