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0
votes
0
replies
97
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago
Chris
▴ 10
3
votes
3
replies
274
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 21 days ago by
ATpoint
★ 4.1k • written 21 days ago by
bioinf
▴ 10
1
vote
1
reply
154
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 23 days ago by
Leo Lahti
▴ 40 • written 24 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2
PCAtools
updated 24 days ago by
Michael Love
42k • written 25 days ago by
Aaliya
• 0
1
vote
3
replies
256
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 24 days ago by
Michael Love
42k • written 25 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
175
views
ATACseq merge peaks
DiffBind
updated 24 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Shloka
• 0
1
vote
2
replies
217
views
Improving the design matrices vignette in RNAseq123
RNAseq123
28 days ago • updated 14 days ago
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago
pl23
• 0
2
votes
9
replies
428
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
Alexandre
• 0
0
votes
0
replies
144
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
25 days ago • updated 17 days ago
glaciya2018
• 0
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
26 days ago • updated 25 days ago
ATpoint
★ 4.1k
0
votes
1
reply
166
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 26 days ago by
Michael Love
42k • written 26 days ago by
kcarey
• 0
0
votes
0
replies
101
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
26 days ago • updated 21 days ago
Sara
• 0
2
votes
5
replies
314
views
get BM error
ensembldb
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Fara
• 0
2
votes
5
replies
262
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 25 days ago by
James W. MacDonald
65k • written 27 days ago by
bandconductor
• 0
0
votes
0
replies
98
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
26 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
238
views
Different Shrunk Log2FC according with reference
DESeq2
updated 26 days ago by
Michael Love
42k • written 26 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
361
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
26 days ago • updated 24 days ago
winwater0928
• 0
3
votes
1
reply
329
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 26 days ago by
Michael Love
42k • written 27 days ago by
i.sudbery
▴ 40
1
vote
2
replies
207
views
Citation for edgeR user guide
edgeR
written 27 days ago by
k___
▴ 30
0
votes
7
replies
758
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 27 days ago
shepherl
3.9k
1
vote
1
reply
135
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
394
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 25 days ago by
swbarnes2
★ 1.4k • written 27 days ago by
Aaliya
• 0
0
votes
0
replies
87
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
27 days ago
info
▴ 10
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData
minfi
updated 26 days ago by
Basti
▴ 780 • written 28 days ago by
clacarion
• 0
0
votes
2
replies
268
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
27 days ago • updated 25 days ago
shuwangxinze1996
• 0
1
vote
2
replies
1.0k
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 27 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 27 days ago by
taur.vil
• 0
3
votes
3
replies
253
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 27 days ago by
Michael Love
42k • written 28 days ago by
WardDeb
• 0
2
votes
4
replies
290
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 28 days ago by
James W. MacDonald
65k • written 4 weeks ago by
Mirella Aurora
• 0
0
votes
1
reply
138
views
FDR via q-value
qvalue
updated 28 days ago by
James W. MacDonald
65k • written 4 weeks ago by
John
• 0
0
votes
5
replies
325
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 26 days ago by
James W. MacDonald
65k • written 29 days ago by
Gayatri
• 0
0
votes
2
replies
245
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 weeks ago • updated 28 days ago
catv
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 28 days ago
shepherl
3.9k
2
votes
13
replies
493
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
29 days ago • updated 26 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
98
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
29 days ago
vaxahey107
• 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago
Chris
▴ 10
0
votes
0
replies
108
views
I am trying to detect alternative splicing.
ASpli
4 weeks ago
Sebashish
• 0
3
votes
2
replies
238
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 28 days ago by
Guido Hooiveld
★ 4.0k • written 4 weeks ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
181
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
bas_work
▴ 30
2
votes
2
replies
227
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
sansan
• 0
1
vote
0
replies
361
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
4 weeks ago
BioinfGuru
▴ 30
4
votes
6
replies
475
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 28 days ago
Jonathan
▴ 10
0
votes
2
replies
151
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
0
votes
3
replies
217
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
prity6459
• 0
5
votes
3
replies
319
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 10 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
4
replies
227
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago
sropri
• 0
0
votes
3
replies
190
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 20 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
0
votes
1
reply
167
views
Adding columns to DEXSeqResults object
DEXSeq
updated 4 weeks ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
45,679 results • Page
3 of 914
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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