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11
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
1 hour ago
bas_work
▴ 30
1
vote
2
replies
56
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 1 hour ago by
James W. MacDonald
65k • written 16 hours ago by
sansan
• 0
1
vote
0
replies
22
views
Tutorial:
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
bioconductor
Install
2 hours ago • updated 1 hour ago
BioinfGuru
▴ 30
0
votes
3
replies
142
views
FilterByExpr low counts with small sample size
edgeR
updated 4 hours ago by
Gordon Smyth
50k • written 1 day ago by
Jonathan
▴ 10
0
votes
2
replies
44
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 hours ago • updated 5 hours ago
prity6459
• 0
0
votes
3
replies
66
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 hours ago by
Gordon Smyth
50k • written 21 hours ago by
prity6459
• 0
0
votes
1
reply
57
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 hours ago by
Gordon Smyth
50k • written 1 day ago by
Shaimaa Gamal
• 0
0
votes
4
replies
70
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
19 hours ago • updated 17 hours ago
sropri
• 0
0
votes
0
replies
23
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
20 hours ago
Mirella Aurora
• 0
0
votes
1
reply
43
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 22 hours ago by
Alejandro Reyes
★ 1.9k • written 1 day ago by
Alessia
• 0
0
votes
1
reply
70
views
Adding columns to DEXSeqResults object
DEXSeq
updated 22 hours ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Clyde
• 0
0
votes
0
replies
31
views
Warning while loading DEP package
DEP
updated 22 hours ago by
shepherl
3.8k • written 22 hours ago by
Namrata
• 0
0
votes
1
reply
48
views
rlog transformation
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
ishij9717
• 0
0
votes
1
reply
45
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
09191919
• 0
0
votes
1
reply
54
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 22 hours ago by
Michael Love
41k • written 2 days ago by
ussarizona
• 0
0
votes
1
reply
73
views
covariate with negative and positive values
DESeq2
updated 22 hours ago by
Michael Love
41k • written 2 days ago by
Brynn
• 0
0
votes
1
reply
74
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
quanah.hudson
• 0
1
vote
2
replies
128
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 18 hours ago
Le
• 0
1
vote
2
replies
85
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago • updated 23 hours ago
Sherin
• 0
0
votes
1
reply
52
views
Input Question for deseq.r
RSeqAn
updated 1 day ago by
ATpoint
★ 4.0k • written 1 day ago by
Nina
• 0
0
votes
3
replies
100
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 6 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
6
replies
153
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
hortense96
• 0
0
votes
0
replies
37
views
News:
Services
flowBeads
2 days ago
creativepeptides2018
• 0
0
votes
0
replies
29
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Enzyme Engineering
BioTIP
2 days ago
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• 0
0
votes
0
replies
35
views
News:
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flowBeads
2 days ago
bocsci11
• 0
0
votes
0
replies
47
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
2 days ago
Maliha Tabassum
• 0
0
votes
4
replies
116
views
flowStats Search Error
flowStats
updated 2 days ago by
shepherl
3.8k • written 3 days ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 1 day ago
shepherl
3.8k
0
votes
1
reply
93
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
tian.liu0720
• 0
1
vote
2
replies
78
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
2 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
70
views
what is the sampleFiles
chipseq
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zhulin
• 0
0
votes
1
reply
109
views
Differentially expressed genes in monocle pseudotime
monocle
updated 3 days ago by
Gordon Smyth
50k • written 5 days ago by
kthapa
• 0
4
votes
8
replies
294
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 14 hours ago by
Peter Hickey
▴ 740 • written 8 days ago by
Juan Higareda
• 0
3
votes
3
replies
136
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 0
0
votes
1
reply
107
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 3 days ago by
kamryncole1963
• 0 • written 8 days ago by
Sara
• 0
0
votes
3
replies
140
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
59
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
3 days ago
Virangika
• 0
0
votes
0
replies
43
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
3 days ago
Henry
▴ 10
1
vote
1
reply
160
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 4 days ago by
Michael Love
41k • written 8 days ago by
Weiqian
▴ 10
0
votes
4
replies
191
views
DEG with low counts
DESeq2
updated 3 hours ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
1
vote
2
replies
226
views
GSVA error
GSVA
5 days ago • updated 3 days ago
Alex
• 0
2
votes
3
replies
245
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 days ago • updated 3 days ago
daniel.carbajo
• 0
3
votes
3
replies
258
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 11 days ago by
Netanel
• 0
1
vote
3
replies
304
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
0
votes
1
reply
667
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
2
replies
153
views
Design Matrix within group comparison more than two groups
DESeq2
6 days ago
hemantcnaik
• 0
0
votes
6
replies
544
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 6 days ago
shepherl
3.8k
2
votes
2
replies
148
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
6 days ago
julia_mcdonough
• 0
45,548 results • Page
1 of 911
Recent ...
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Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize
by
James W. MacDonald
65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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