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0
replies
14
views
Dominance Index for Shotgun Metagenomics Data
microbiome
4 hours ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
70
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 3 hours ago by
Michael Love
41k • written 20 hours ago by
JalapenoCornbread
• 0
0
votes
6
replies
106
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
updated 18 hours ago by
James W. MacDonald
65k • written 22 hours ago by
pl23
• 0
2
votes
9
replies
262
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 20 hours ago by
James W. MacDonald
65k • written 1 day ago by
Alexandre
• 0
0
votes
0
replies
34
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
1 day ago
glaciya2018
• 0
0
votes
2
replies
72
views
PCA plot suggestions
DESeq2
PCAtools
updated 43 minutes ago by
Michael Love
41k • written 1 day ago by
Aaliya
• 0
0
votes
1
reply
80
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
kcarey
• 0
0
votes
1
reply
42
views
ATACseq merge peaks
DiffBind
updated 3 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
Shloka
• 0
0
votes
0
replies
24
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
2 days ago
Sara
• 0
0
votes
0
replies
33
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
2 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
91
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
2 days ago • updated 1 day ago
ATpoint
★ 4.0k
1
vote
3
replies
109
views
Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
179
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 9 hours ago
winwater0928
• 0
2
votes
5
replies
154
views
get BM error
ensembldb
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
Fara
• 0
2
votes
5
replies
148
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 23 hours ago by
James W. MacDonald
65k • written 2 days ago by
bandconductor
• 0
1
vote
1
reply
86
views
Citation for edgeR user guide
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
k___
▴ 30
3
votes
1
reply
219
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
i.sudbery
▴ 40
1
vote
1
reply
63
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
240
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 day ago by
swbarnes2
★ 1.3k • written 3 days ago by
Aaliya
• 0
0
votes
0
replies
29
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
3 days ago
info
▴ 10
0
votes
2
replies
128
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
3 days ago • updated 1 day ago
shuwangxinze1996
• 0
0
votes
1
reply
97
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
taur.vil
• 0
3
votes
3
replies
172
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
WardDeb
• 0
1
vote
4
replies
140
views
minfi::read.metharray.exp
minfiData
minfi
updated 2 days ago by
Basti
▴ 780 • written 4 days ago by
clacarion
• 0
0
votes
1
reply
88
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 7 hours ago by
Gordon Smyth
50k • written 4 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
230
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 2 days ago by
James W. MacDonald
65k • written 4 days ago by
Gayatri
• 0
1
vote
13
replies
278
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
0
votes
0
replies
44
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
5 days ago
vaxahey107
• 0
12
votes
12
replies
785
views
Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by
Robert Castelo
★ 3.3k • written 6 days ago by
Chris
• 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
6 days ago
Sebashish
• 0
3
votes
2
replies
165
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
86
views
FDR via q-value
qvalue
updated 4 days ago by
James W. MacDonald
65k • written 6 days ago by
John
• 0
0
votes
2
replies
156
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
7 days ago • updated 4 days ago
catv
• 0
1
vote
0
replies
208
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
7 days ago • updated 6 days ago
BioinfGuru
▴ 30
1
vote
4
replies
158
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 3 days ago by
James W. MacDonald
65k • written 7 days ago by
Mirella Aurora
• 0
4
votes
6
replies
338
views
FilterByExpr low counts with small sample size
edgeR
8 days ago • updated 4 days ago
Jonathan
▴ 10
0
votes
4
replies
199
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 days ago • updated 6 days ago
lonn
• 0
1
vote
2
replies
118
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 days ago • updated 1 hour ago
ussarizona
▴ 10
0
votes
7
replies
254
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
9 days ago • updated 3 days ago
hortense96
• 0
1
vote
2
replies
221
views
How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago
Weiqian
▴ 10
3
votes
3
replies
294
views
permutation test in edgeR
rna-seq
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 18 days ago by
Netanel
• 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
27 days ago • updated 6 days ago
Chris
• 0
0
votes
7
replies
619
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 2 days ago
shepherl
3.8k
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 4 days ago
shepherl
3.8k
0
votes
2
replies
767
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
1
vote
3
replies
817
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 2 days ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
932
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 3 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 4 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
52 results • Page
1 of 2
Recent ...
Replies
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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