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Votes
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.6 years ago by
o.giannakopoulou
▴ 10
9
votes
11
replies
6.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 10 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 11 months ago by
snow34
• 0 • written 6.7 years ago by
ap3637
• 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.3 years ago by
chandlerjd58
▴ 10
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 6 days ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
2
votes
2
replies
418
views
"Details" section for specific software packages
Website
updated 7 months ago by
Mike Smith
★ 6.5k • written 7 months ago by
Justin
• 0
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
2
replies
248
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
8 weeks ago • updated 7 weeks ago
w.cookson
• 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
10 months ago
Luca
• 0
0
votes
2
replies
1.4k
views
Error: BiocParallel errors
xcms
msdata
BiocParallel
8 months ago
mavamay
• 0
0
votes
2
replies
175
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 9 days ago by
zhouwanding
▴ 10 • written 11 days ago by
Seungmin
• 0
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2
lowcount
updated 4 months ago by
Xiao
• 0 • written 9.2 years ago by
aristotele_m
▴ 40
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by
serpalma.v
▴ 60
1
vote
3
replies
554
views
Merging Methylation data (M-values) with phenotypic data
MethylationArrayData
methylationArrayAnalysis
updated 9 months ago by
James W. MacDonald
66k • written 9 months ago by
hayleyw
• 0
0
votes
3
replies
11k
views
SingleR Label.Ont
SingleR
updated 12 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
11
votes
10
replies
7.6k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 9 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 20
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 19 months ago by
jeremymsimon
▴ 20
2
votes
6
replies
402
views
Factor vs Character in design
DESeq2
11 weeks ago
James Aiden
• 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 23 months ago by
Mohamed
▴ 30
2
votes
5
replies
1.4k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Sara
• 0
0
votes
2
replies
572
views
Heat Map
ColData
pheatmap
DESeq2
written 11 months ago by
dania.khalid
• 0
7
votes
6
replies
4.3k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 7 months ago by
Marcel Ramos
700 • written 21 months ago by
Recep
▴ 20
1
vote
4
replies
707
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
7 months ago
andrew.b.kleist
▴ 10
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
10 months ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
893
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by
Michael Love
42k • written 9 months ago by
Juan Pablo
• 0
6
votes
12
replies
5.2k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
7 months ago • updated 4 weeks ago
shepherl
3.9k
2
votes
6
replies
1.6k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 7 weeks ago by
Tim Peters
▴ 180 • written 6 months ago by
rae.alshammari
▴ 10
2
votes
2
replies
239
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
sansan
• 0
1
vote
3
replies
521
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 5 months ago by
malliardtee
• 0 • written 5 months ago by
Guangsheng
• 0
0
votes
2
replies
603
views
MIcrosynteny block information - Syntenet
syntenet
microsynteny
blocks
synteny
written 10 months ago by
Alexandros
• 0
2
votes
2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.5 years ago by
Dario Strbenac
★ 1.5k
2
votes
7
replies
2.5k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 7 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
1
vote
2
replies
718
views
DESeq2 batch design
DESeq2
updated 9 months ago by
swbarnes2
★ 1.4k • written 9 months ago by
Hope
▴ 10
4
votes
7
replies
913
views
weird volcano plot
DESeq2
updated 11 weeks ago by
Shuning
• 0 • written 6 months ago by
shouzheng
▴ 10
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 7 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
1
vote
7
replies
895
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 5 months ago by
Gordon Smyth
50k • written 7 months ago by
Gimena
• 0
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by
Dimitris
• 0 • written 10.9 years ago by
Makis Motakis
▴ 30
0
votes
2
replies
438
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 5 months ago by
Stephanie M. Gogarten
▴ 870 • written 5 months ago by
Mindy wang
• 0
0
votes
5
replies
721
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout
DESeq2
written 11 months ago by
Lillian
• 0
0
votes
2
replies
308
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
z_bahari
• 0
0
votes
2
replies
885
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 10 months ago by
Malcolm Cook
★ 1.6k • written 10 months ago by
Nebat
• 0
2
votes
2
replies
338
views
locfunc not found in DESeq2
locfunc
DESeq2
shorth
estimateSizeFactors
3 months ago
Hope
▴ 10
0
votes
2
replies
183
views
DESeq2 v1.35.0
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
Espresso
• 0
3
votes
3
replies
436
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
1
vote
8
replies
1.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 11 months ago by
sean.mccutcheon
• 0
2
votes
3
replies
3.1k
views
Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by
pbachali
▴ 50
2
votes
7
replies
4.8k
views
Installing Local packages in Bioconductor
package
updated 9 months ago by
Boxun
• 0 • written 2.0 years ago by
BioC123
• 0
0
votes
5
replies
575
views
Unexpected results for a differential expression analysis between males and females
DESeq2
updated 5 months ago by
Robert Castelo
★ 3.3k • written 5 months ago by
Loïc
• 0
1
vote
2
replies
125
views
Subsetting RNAseq data | voomaByGroup()
limma
5 days ago • updated 3 days ago
Anna
• 0
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.6 years ago by
bharata1803
▴ 60
1,745 results • Page
2 of 35
Recent ...
Replies
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
Wei Shi
★ 3.6k
Your bam file names should be stored in a vector and then provided to the `files` parameter.
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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