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15
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 9 days ago
shepherl
3.8k
7
votes
28
replies
6.0k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 7 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
21
replies
6.4k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 4 months ago by
Marge
• 0 • written 11.2 years ago by
José Luis Lavín
▴ 280
1
vote
8
replies
1.4k
views
News:
Final List of Deprecated Package Bioc 3.9
deprecation
release
software
experimentData
News
written 5.0 years ago by
shepherl
3.8k
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 19 days ago by
ama304374
• 0 • written 6.2 years ago by
daijieqiong
▴ 10
1
vote
6
replies
2.6k
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 7.4 years ago by
Camila Orellana
▴ 10
4
votes
16
replies
7.2k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 6 days ago by
Shaimaa Gamal
• 0 • written 8.9 years ago by
Pauly Lin
▴ 150
0
votes
5
replies
5.7k
views
masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
masigpro
updated 7 months ago by
Tatsuya
• 0 • written 8.8 years ago by
john
▴ 120
2
votes
9
replies
1.1k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 5 months ago by
Erqiang Hu
▴ 50 • written 5 months ago by
jovel_juan
▴ 30
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 4 weeks ago by
Michael Love
41k • written 7.8 years ago by
adesrichard
▴ 30
0
votes
5
replies
1.1k
views
pathway finding software
written 15.4 years ago by
Yanqin Yang
▴ 250
2
votes
11
replies
1.5k
views
Not able to download recount3 data
recount3
updated 10 months ago by
Leonardo Collado Torres
★ 1.0k • written 15 months ago by
Niveditha
▴ 20
3
votes
5
replies
1.6k
views
Error: 'IdClusters'
DECIPHER
updated 10 months ago by
Ling-Hsiu
▴ 10 • written 13 months ago by
julieta.micorriza
• 0
0
votes
7
replies
334
views
DESeq2 filtering vs edgeR filtering
DESeq2
14 days ago • updated 1 day ago
fr8712ca-s
• 0
1
vote
3
replies
2.9k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 9 days ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
0
votes
11
replies
3.6k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 8 weeks ago by
Tim Peters
▴ 160 • written 7.0 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 10.2 years ago by
Guest User
★ 13k
0
votes
11
replies
1.2k
views
Unable to install DESeq2
DESeq2
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
luis.franco
• 0
4
votes
3
replies
734
views
WGCNA documentation not available
WGCNA
written 3 months ago by
ramonmassoni
▴ 10
2
votes
6
replies
1.2k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 10 months ago by
Leonardo Collado Torres
★ 1.0k • written 15 months ago by
Max Bone
• 0
2
votes
3
replies
1.3k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
gingergeiger22
• 0
0
votes
4
replies
701
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
10 months ago
sreeshmaraj72
• 0
1
vote
8
replies
245
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 hours ago by
Gordon Smyth
50k • written 1 day ago by
Amit
• 0
9
votes
11
replies
5.5k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 15 days ago by
shepherl
3.8k • written 2.2 years ago by
jon.klonowski
▴ 40
0
votes
3
replies
1.4k
views
extract rsids of SNPs using their genomic positions
rsids
SNPlocs.Hsapiens.dbSNP150.GRCh38
written 8 months ago by
olgadolgova
• 0
1
vote
10
replies
1.9k
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
written 16 months ago by
Alexandros
• 0
4
votes
10
replies
1.7k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 5 months ago by
shepherl
3.8k • written 18 months ago by
Florian Finkernagel
▴ 30
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
4
replies
2.2k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 16 months ago by
Sarah
• 0
0
votes
6
replies
1.3k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 11 months ago by
yrkkhdesiserials
• 0 • written 2.6 years ago by
memy
• 0
4
votes
13
replies
1.2k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 months ago by
Michael Love
41k • written 7 months ago by
Christian
• 0
2
votes
3
replies
1.0k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 10 weeks ago by
Alex
• 0 • written 2.7 years ago by
Paul Shannon
▴ 470
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 8 months ago by
Charles Plessy
▴ 180 • written 16 months ago by
Meng
▴ 30
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 12 weeks ago by
Matthias Lienhard
▴ 240 • written 7.0 years ago by
justinburgener
▴ 20
2
votes
3
replies
753
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 7 months ago by
Vitor
• 0
1
vote
13
replies
10k
views
unable to access index for repository
Bioconductor
ConsensusClusterPlus
updated 7 months ago by
Mehdi
• 0 • written 15 months ago by
k.wickstrom
• 0
5
votes
11
replies
4.1k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.8 years ago by
seeker
• 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 26 days ago by
Gordon Smyth
50k • written 18.9 years ago by
SAURIN
★ 1.1k
3
votes
4
replies
2.9k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.6 years ago by
Patrick
• 0
2
votes
6
replies
2.4k
views
RNA-seq analysis across different experiments
limma
deseq2
normalization
degenes
design and contrast matrix
written 6.7 years ago by
mrigaya.mehra
▴ 10
1
vote
7
replies
2.8k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 7 months ago by
lucap
• 0 • written 2.9 years ago by
Marianna
▴ 10
1
vote
5
replies
1.6k
views
rowsum or similar for RleArray?
delayedarray
rowsum
written 6.6 years ago by
maltethodberg
▴ 170
1
vote
16
replies
3.0k
views
error in ChAMP loading file
ChAMP
updated 15 days ago by
hortenseguillaume96
• 0 • written 16 months ago by
Giulia
• 0
0
votes
3
replies
2.4k
views
Background correction with neqc
Normalization
Cancer
Normalization
Cancer
updated 4 months ago by
Gordon Smyth
50k • written 12.3 years ago by
Guest User
★ 13k
14
votes
5
replies
21k
views
Dealing with genes that have Padj=NA
deseq2
updated 7 months ago by
Juan Pablo
• 0 • written 8.3 years ago by
raya.fai
▴ 60
1
vote
4
replies
5.9k
views
Error loading impute(): '/usr/lib/libgfortran.5.dylib' (no such file)
Install
impute
updated 11 months ago by
yuzhijian
• 0 • written 2.1 years ago by
Aaron
• 0
0
votes
6
replies
1.4k
views
mailman bugs
Website
21.1 years ago • updated 9 months ago
Gordon Smyth
50k
3
votes
7
replies
5.3k
views
error with champ.load
champ
written 6.4 years ago by
o.giannakopoulou
▴ 10
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 8 months ago by
Gordon Smyth
50k • written 11.9 years ago by
Kripa R
▴ 180
0
votes
7
replies
1.3k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install
instal
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
client.kashi
• 0
1,736 results • Page
1 of 35
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Answer: Merging featureCounts output for different species
by
Michael Love
41k
Bioconductor support site is for posting questions about software. Try biostars.
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
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