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News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 26 days ago
shepherl
3.9k
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 2 days ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
7
votes
6
replies
568
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 1 hour ago by
jane
• 0 • written 14 days ago by
robersy
• 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 5 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 27 days ago
shepherl
3.9k
1
vote
2
replies
407
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
Kim
• 0
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 19 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 2 days ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
4
votes
5
replies
330
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
14 days ago • updated 4 days ago
Chris
▴ 10
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 19 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 14 days ago
Henrik Bengtsson
★ 2.4k
0
votes
2
replies
133
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 5 days ago by
zhouwanding
▴ 10 • written 7 days ago by
Seungmin
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 2 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
3
votes
4
replies
287
views
Store output of matchPWM()
biostrings
Biostrings
18 days ago • updated 6 days ago
mat149
▴ 70
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
29 days ago • updated 18 days ago
Chris
▴ 10
0
votes
3
replies
9.0k
views
SingleR Label.Ont
SingleR
updated 8 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
2
replies
169
views
DESeq2 v1.35.0
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
Espresso
• 0
0
votes
6
replies
297
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 15 days ago by
swbarnes2
★ 1.4k • written 17 days ago by
arfranco
▴ 130
2
votes
4
replies
286
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
Mirella Aurora
• 0
4
votes
9
replies
493
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 12 days ago
Juan Higareda
• 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 29 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 12 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
1
vote
2
replies
747
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 23 days ago
Patadù
▴ 10
1
vote
1
reply
154
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 23 days ago by
Leo Lahti
▴ 40 • written 23 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 9 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 12 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
5
votes
3
replies
313
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
2
votes
1
reply
146
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 13 days ago by
Michael Love
42k • written 13 days ago by
mat149
▴ 70
3
votes
3
replies
271
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
bioinf
▴ 10
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 26 days ago by
i.sudbery
▴ 40
0
votes
7
replies
366
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 26 days ago
hortense96
• 0
4
votes
2
replies
631
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
17 days ago • updated 13 days ago
gene_bioconductor
▴ 10
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
19 days ago • updated 16 days ago
Aurora
• 0
1
vote
2
replies
132
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
5 days ago • updated 4 days ago
Daniel
• 0
2
votes
3
replies
127
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
Guillermo
• 0
0
votes
4
replies
377
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 8 days ago by
Ziliang
• 0 • written 18 days ago by
Ian D.
▴ 70
2
votes
9
replies
427
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
Alexandre
• 0
0
votes
1
reply
173
views
ATACseq merge peaks
DiffBind
updated 23 days ago by
ATpoint
★ 4.1k • written 25 days ago by
Shloka
• 0
1
vote
4
replies
233
views
minfi::read.metharray.exp
minfiData
minfi
updated 25 days ago by
Basti
▴ 780 • written 27 days ago by
clacarion
• 0
1
vote
2
replies
216
views
Improving the design matrices vignette in RNAseq123
RNAseq123
27 days ago • updated 13 days ago
Lluís Revilla Sancho
▴ 730
0
votes
2
replies
752
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 4 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
205
views
Citation for edgeR user guide
edgeR
written 26 days ago by
k___
▴ 30
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 6 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
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
4
votes
9
replies
258
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
pangtaihin
• 0
0
votes
8
replies
507
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 5 days ago by
BioinfGuru
▴ 30 • written 6 days ago by
Eric Katagirya
• 0
1
vote
7
replies
359
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
24 days ago • updated 23 days ago
pl23
• 0
0
votes
5
replies
325
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 25 days ago by
James W. MacDonald
65k • written 28 days ago by
Gayatri
• 0
169 results • Page
1 of 4
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
jane
• 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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