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18
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2.9k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 15 days ago
shepherl
3.9k
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 12 weeks ago by
Gordon Smyth
50k • written 9.2 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
7
replies
687
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 9 days ago
shepherl
3.9k
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 5 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
2
votes
6
replies
2.5k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error
cn.mops
updated 7 weeks ago by
ama304374
• 0 • written 6.3 years ago by
daijieqiong
▴ 10
1
vote
8
replies
1.5k
views
News:
Final List of Deprecated Package Bioc 3.9
deprecation
release
software
experimentData
News
written 5.1 years ago by
shepherl
3.9k
0
votes
7
replies
429
views
DESeq2 filtering vs edgeR filtering
DESeq2
7 weeks ago • updated 5 weeks ago
fr8712ca-s
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
0
votes
5
replies
1.1k
views
pathway finding software
written 15.5 years ago by
Yanqin Yang
▴ 250
3
votes
5
replies
1.7k
views
Error: 'IdClusters'
DECIPHER
updated 11 months ago by
Ling-Hsiu
▴ 10 • written 14 months ago by
julieta.micorriza
• 0
2
votes
11
replies
1.6k
views
Not able to download recount3 data
recount3
updated 12 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
Niveditha
▴ 20
0
votes
5
replies
5.8k
views
masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
masigpro
updated 9 months ago by
Tatsuya
• 0 • written 8.9 years ago by
john
▴ 120
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 6 weeks ago by
Shaimaa Gamal
• 0 • written 9.0 years ago by
Pauly Lin
▴ 150
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.5 years ago by
Camila Orellana
▴ 10
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 10 weeks ago by
Michael Love
41k • written 7.9 years ago by
adesrichard
▴ 30
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 6 months ago by
Erqiang Hu
▴ 50 • written 6 months ago by
jovel_juan
▴ 30
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 6 weeks ago by
snijesh
▴ 20 • written 6.6 years ago by
Ramiro Magno
▴ 100
0
votes
11
replies
3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 170 • written 7.1 years ago by
Jenny Drnevich
★ 2.0k
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation
affy
oligo
ffpe
Annotation
affy
oligo
ffpe
written 10.3 years ago by
Guest User
★ 13k
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor
ConsensusClusterPlus
updated 8 months ago by
Mehdi
• 0 • written 16 months ago by
k.wickstrom
• 0
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
luis.franco
• 0
2
votes
3
replies
805
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 8 months ago by
Vitor
• 0
0
votes
6
replies
1.5k
views
mailman bugs
Website
21.2 years ago • updated 10 months ago
Gordon Smyth
50k
1
vote
10
replies
2.0k
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
written 17 months ago by
Alexandros
• 0
0
votes
6
replies
1.2k
views
LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?
affy
affy
updated 8 weeks ago by
Gordon Smyth
50k • written 19.0 years ago by
SAURIN
★ 1.1k
0
votes
4
replies
740
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
11 months ago
sreeshmaraj72
• 0
1
vote
5
replies
1.7k
views
rowsum or similar for RleArray?
delayedarray
rowsum
written 6.7 years ago by
maltethodberg
▴ 180
4
votes
3
replies
916
views
WGCNA documentation not available
WGCNA
written 4 months ago by
ramonmassoni
▴ 10
0
votes
3
replies
1.7k
views
extract rsids of SNPs using their genomic positions
rsids
SNPlocs.Hsapiens.dbSNP150.GRCh38
written 9 months ago by
olgadolgova
• 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by
Juan Pablo
• 0 • written 8.4 years ago by
raya.fai
▴ 60
1
vote
4
replies
2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 17 months ago by
Sarah
• 0
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by
Gordon Smyth
50k • written 12.0 years ago by
Kripa R
▴ 180
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 3 months ago by
Alex
• 0 • written 2.8 years ago by
Paul Shannon
▴ 470
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.9k • written 19 months ago by
Florian Finkernagel
▴ 30
9
votes
11
replies
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 7 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
2
votes
3
replies
683
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago
Gerhard Thallinger
▴ 180
2
votes
8
replies
519
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by
o.giannakopoulou
▴ 10
0
votes
7
replies
1.6k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install
instal
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
client.kashi
• 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization
Cancer
Normalization
Cancer
updated 6 months ago by
Gordon Smyth
50k • written 12.4 years ago by
Guest User
★ 13k
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 28 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 12 months ago by
Leonardo Collado Torres
★ 1.0k • written 17 months ago by
Max Bone
• 0
6
votes
5
replies
1.1k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 7 months ago by
Peter Hickey
▴ 740 • written 9 months ago by
richardallenfriedmanbrooklyn
▴ 20
1
vote
9
replies
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 6.2 years ago by
klalit1803
• 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.0 years ago by
Marianna
▴ 20
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by
Charles Plessy
▴ 180 • written 17 months ago by
Meng
▴ 30
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
0
votes
11
replies
2.0k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.6 years ago by
mike Ad.
▴ 30
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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