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Views
Votes
0
votes
0
replies
63
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
7 days ago
taylor.witte
• 0
0
votes
0
replies
79
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
7 days ago
erbrocato
• 0
1
vote
2
replies
158
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 days ago by
ATpoint
★ 4.0k • written 8 days ago by
maximilian.beikirch
• 0
0
votes
3
replies
176
views
Help with Complex DESeq2 Design
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
kelsey.beavers
• 0
0
votes
2
replies
134
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 days ago • updated 8 days ago
rocanja
▴ 60
0
votes
2
replies
138
views
Visium RNA
metaMSdata
updated 8 days ago by
vvvc360work2
• 0 • written 8 days ago by
Karlison
• 0
4
votes
7
replies
611
views
DESeq2 unable to handle large count values
DESeq2
updated 8 days ago by
Michael Love
41k • written 4 months ago by
robennet
• 0
0
votes
0
replies
67
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 days ago
BID
• 0
4
votes
3
replies
158
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 9 days ago by
Georg
• 0
0
votes
5
replies
9.1k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 8 days ago by
Eva
• 0 • written 7.5 years ago by
ctl
• 0
0
votes
2
replies
1.0k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 9 days ago by
william
• 0 • written 17 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
109
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
23 days ago • updated 9 days ago
Giovanni Calice
▴ 160
0
votes
1
reply
238
views
News:
BioC2024 abstract submission is open!
BioC2024
Conference
Bioconductor
updated 9 days ago by
howell
• 0 • written 5 weeks ago by
Maria Doyle
▴ 70
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
2
votes
3
replies
217
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
JKim
• 0
0
votes
3
replies
1.3k
views
Error in ImportRData
dplyr
IsoformSwitchAnalyzeR
written 11 months ago by
ramon.dslps
• 0
1
vote
2
replies
617
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 8 months ago by
malat1_t
▴ 10
0
votes
1
reply
1.0k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST
AIC calcuation
Parameters
single cell
hurdle model
updated 9 days ago by
rproendo
▴ 20 • written 5.1 years ago by
mcalgaro93
• 0
2
votes
2
replies
182
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
10 days ago • updated 9 days ago
Eva
▴ 10
2
votes
5
replies
1.2k
views
Downloading count matrix for full recount3 dataset
recount3
updated 9 days ago by
Leonardo Collado Torres
★ 1.0k • written 2.7 years ago by
Ben
• 0
3
votes
15
replies
2.6k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 9 days ago
shepherl
3.8k
1
vote
1
reply
121
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Emma
• 0
0
votes
1
reply
97
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 10 days ago by
Michael Love
41k • written 10 days ago by
rahaf.nazzal9
• 0
2
votes
2
replies
196
views
between lane normalization upper quantile
EDASeq
edgeR
13 days ago • updated 10 days ago
elesofi
• 0
0
votes
1
reply
115
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Yuqin
• 0
1
vote
7
replies
1.1k
views
enrichGOgradient color change
clusterProfiler
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
inna.gur
• 0
1
vote
5
replies
327
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
20 days ago • updated 10 days ago
Gerhard Thallinger
▴ 180
0
votes
1
reply
125
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 11 days ago by
Simon Pearce
• 0 • written 7 weeks ago by
User3088
• 0
0
votes
1
reply
124
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
159
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
13 days ago • updated 11 days ago
feather-W
• 0
0
votes
1
reply
143
views
Exact same results in Diffbind with different normalization methods
DiffBind
16 days ago • updated 11 days ago
red_bricks
▴ 50
2
votes
3
replies
2.1k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 11 days ago by
ATpoint
★ 4.0k • written 24 months ago by
liqidong52
▴ 20
1
vote
3
replies
313
views
DEseq2 coefficient
DESeq2
coefficient
4 weeks ago • updated 12 days ago
JKim
• 0
0
votes
2
replies
211
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
z_bahari
• 0
1
vote
1
reply
133
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
zoheir.alayash
▴ 10
3
votes
1
reply
1.7k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 13 days ago by
zoheir.alayash
▴ 10 • written 2.0 years ago by
S T
▴ 90
4
votes
4
replies
1.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 13 days ago by
feather-W
• 0 • written 11 months ago by
Bernardo
▴ 10
0
votes
1
reply
632
views
gwas power calculation for quantitative traits
power
GWAS
written 2.6 years ago by
rajya82
• 0
0
votes
4
replies
350
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
Jad
• 0
0
votes
1
reply
127
views
problem with ClusterRepro function
WGCNA
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Antonio.Aubry
• 0
0
votes
2
replies
157
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
14 days ago • updated 13 days ago
kcarey
• 0
0
votes
2
replies
246
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 15 days ago by
gglatzer
• 0
2
votes
2
replies
186
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
14 days ago
Sabiha
▴ 20
0
votes
2
replies
172
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
15 days ago • updated 14 days ago
Sam
▴ 10
4
votes
6
replies
577
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 15 days ago by
Akshay
• 0 • written 4 months ago by
Sarah
▴ 10
6
votes
9
replies
4.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
updated 15 days ago by
Melissa
• 0 • written 5 months ago by
shepherl
3.8k
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
2
votes
5
replies
1.7k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 15 days ago by
James W. MacDonald
65k • written 11 months ago by
angel
• 0
0
votes
1
reply
165
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 16 days ago by
BioinfoMug
• 0
1
vote
1
reply
166
views
i'm not getting any differentially expressed genes.
DESeq2
updated 15 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Marilyn
• 0
1,735 results • Page
2 of 35
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
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…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
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
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