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Rank
Views
Votes
2
votes
2
replies
93
views
fgsea significant result
fgsea
1 day ago • updated 16 hours ago
Chris
• 0
0
votes
3
replies
165
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 18 days ago by
Alessia
• 0
1
vote
2
replies
712
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago
ussarizona
▴ 10
1
vote
2
replies
139
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
19 days ago
Ana
• 0
1
vote
2
replies
296
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 2 days ago
Kim
• 0
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 17 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
8
votes
23
replies
947
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 24 days ago by
Robert Castelo
★ 3.3k • written 25 days ago by
Bine
▴ 40
1
vote
4
replies
325
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
12 days ago • updated 10 days ago
winwater0928
• 0
0
votes
3
replies
247
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
HAK
• 0
1
vote
1
reply
186
views
Differentially expressed genes in monocle pseudotime
monocle
updated 20 days ago by
Gordon Smyth
50k • written 22 days ago by
kthapa
• 0
0
votes
3
replies
153
views
Store output of matchPWM()
biostrings
Biostrings
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
mat149
▴ 70
3
votes
3
replies
227
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
WardDeb
• 0
1
vote
1
reply
169
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 10 days ago by
Gordon Smyth
50k • written 14 days ago by
Lluís Revilla Sancho
▴ 730
3
votes
1
reply
312
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
i.sudbery
▴ 40
0
votes
1
reply
135
views
ATACseq merge peaks
DiffBind
updated 9 days ago by
ATpoint
★ 4.1k • written 11 days ago by
Shloka
• 0
0
votes
1
reply
135
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
angelathuynh5
• 0
0
votes
4
replies
601
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 19 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
5
votes
6
replies
426
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 23 days ago by
ATpoint
★ 4.1k • written 26 days ago by
nhaus
▴ 30
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 5 days ago
Chris
• 0
0
votes
1
reply
180
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
BCS12
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 3 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
2
votes
3
replies
124
views
package goseq seems to be not available on the latest version of R
goseq
updated 1 minute ago by
Gordon Smyth
50k • written 2 days ago by
Patrycja
▴ 20
3
votes
1
reply
465
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 6 hours ago by
Gordon Smyth
50k • written 3 days ago by
gene_bioconductor
▴ 10
0
votes
1
reply
164
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 26 days ago by
Michael Love
41k • written 26 days ago by
Adelaide
• 0
0
votes
1
reply
112
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 17 days ago by
Michael Love
41k • written 18 days ago by
09191919
• 0
0
votes
4
replies
313
views
Help with design.matrix
limma
4 weeks ago • updated 29 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
101
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Agung
• 0
0
votes
3
replies
239
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
SSSJec
• 0
0
votes
1
reply
102
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
z_bahari
• 0
2
votes
2
replies
193
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
23 days ago
julia_mcdonough
• 0
1
vote
3
replies
214
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
518
views
GSVA error
GSVA
22 days ago • updated 20 days ago
Alex
• 0
0
votes
2
replies
220
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
nhaus
▴ 30
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 5 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
3
votes
1
reply
755
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
0
replies
132
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
25 days ago
Eryn
• 0
1
vote
2
replies
157
views
Error in champ.load(): The following specified files do not exist
ChAMP
18 days ago • updated 17 days ago
Sherin
• 0
0
votes
0
replies
124
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
11 days ago • updated 3 days ago
glaciya2018
• 0
0
votes
3
replies
132
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
0
replies
86
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
25 days ago
Dennis
• 0
0
votes
0
replies
84
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
23 days ago
shepherl
3.9k
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
20 days ago
Virangika
• 0
0
votes
0
replies
99
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
24 days ago
communication
• 0
0
votes
0
replies
21
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
14 hours ago
robersy
• 0
0
votes
0
replies
61
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
5 days ago
Maria Doyle
▴ 70
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
24 days ago
Stevie Pederson
• 0
0
votes
1
reply
58
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by
4r-rtg
• 0
0
votes
0
replies
97
views
I am trying to detect alternative splicing.
ASpli
15 days ago
Sebashish
• 0
0
votes
0
replies
80
views
News:
Services
flowBeads
19 days ago
creativepeptides2018
• 0
0
votes
0
replies
82
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
15 days ago
vaxahey107
• 0
191 results • Page
3 of 4
Recent ...
Replies
Comment: Couldn't connect to server while using "pathways"
by
ATpoint
★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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