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0
votes
1
reply
68
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
8 hours ago • updated 7 hours ago
minardsmitha
▴ 10
0
votes
1
reply
40
views
recount3 problem downloading data from source sra
recount3
updated 6 hours ago by
Leonardo Collado Torres
★ 1.0k • written 9 hours ago by
PABLO ANTONIO
• 0
0
votes
0
replies
20
views
Conditional analysis
GENESIS
10 hours ago
SuperDad
• 0
0
votes
0
replies
21
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
11 hours ago • updated 9 hours ago
Raghad
• 0
1
vote
1
reply
43
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
updated 11 hours ago by
James W. MacDonald
66k • written 12 hours ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
50
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 9 hours ago by
James W. MacDonald
66k • written 1 day ago by
Tim Barry
• 0
0
votes
2
replies
69
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
written 1 day ago by
landenshanie
▴ 40
0
votes
0
replies
21
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
1 day ago
pierre.devillemereuil
• 0
0
votes
1
reply
48
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
V_Vibes
• 0
1
vote
1
reply
68
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 1 day ago by
James W. MacDonald
66k • written 1 day ago by
Đình Vinh
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
1 day ago
shahrozimmac
0
1
vote
1
reply
169
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 1 day ago by
James W. MacDonald
66k • written 1 day ago by
ttt
• 0
0
votes
0
replies
30
views
Processing of curatedmetagenomics
curatedMetagenomicData
1 day ago
Edward
• 0
1
vote
3
replies
113
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
boczniak767
▴ 720
0
votes
2
replies
73
views
How to run allelic imbalance in apeglm
apeglm
updated 1 day ago by
Michael Love
42k • written 2 days ago by
euge.eugenio
▴ 20
0
votes
0
replies
36
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
2 days ago
Bibi
• 0
0
votes
5
replies
158
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
2 days ago • updated 1 day ago
Galina
• 0
1
vote
2
replies
107
views
Subsetting RNAseq data | voomaByGroup()
limma
3 days ago • updated 1 day ago
Anna
• 0
0
votes
1
reply
69
views
ERROR; return code from pthread_create() is 22
affy
updated 1 day ago by
James W. MacDonald
66k • written 3 days ago by
pickingastar
• 0
0
votes
0
replies
49
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
3 days ago • updated 2 days ago
Abiologist
• 0
2
votes
4
replies
195
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 1 day ago by
Michael Love
42k • written 4 days ago by
shaunpeterson
• 0
0
votes
3
replies
123
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 4 days ago by
damian.szk
▴ 80 • written 4 days ago by
ninidea
• 0
0
votes
6
replies
563
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 1 day ago
Ken C
• 0
0
votes
2
replies
135
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
5 days ago
makala
• 0
0
votes
0
replies
63
views
determine k during RUVSeq
RUVSeq
RUVnormalize
5 days ago
Ειρήνη
• 0
0
votes
0
replies
64
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
5 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
15
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
5 days ago
oliverelijhan
0
0
votes
0
replies
93
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
5 days ago
Anton01
• 0
2
votes
3
replies
153
views
Problem installing ChAMP on a MacBook
ChAMP
updated 5 days ago by
shepherl
3.9k • written 5 days ago by
Galia
• 0
0
votes
0
replies
58
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
6 days ago
danalvoronov
▴ 10
0
votes
0
replies
59
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
6 days ago
k200987
• 0
2
votes
5
replies
244
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
6 days ago • updated 4 days ago
Patadù
▴ 10
0
votes
4
replies
160
views
error running enricher from clusterprofiler
clusterProfiler
cluster
6 days ago
Yael
• 0
2
votes
3
replies
156
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
Guillermo
• 0
0
votes
0
replies
50
views
Difference in Contrast in DiffBind
DiffBind
6 days ago
zzrammal
• 0
4
votes
9
replies
294
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
pangtaihin
• 0
1
vote
2
replies
125
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
6 days ago
Patadù
▴ 10
0
votes
3
replies
141
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 6 days ago by
Michael Love
42k • written 7 days ago by
Kasper
• 0
1
vote
2
replies
149
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
7 days ago • updated 6 days ago
Daniel
• 0
1
vote
0
replies
78
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
7 days ago
Aleena
▴ 30
0
votes
0
replies
64
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
7 days ago
Researcher
• 0
1
vote
3
replies
265
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Ashley
• 0
1
vote
2
replies
264
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
8 days ago • updated 5 days ago
BioinfGuru
▴ 30
0
votes
8
replies
537
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 7 days ago by
BioinfGuru
▴ 30 • written 8 days ago by
Eric Katagirya
• 0
0
votes
1
reply
108
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 7 days ago by
Michael Love
42k • written 8 days ago by
piemmea
• 0
0
votes
2
replies
117
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
8 days ago • updated 7 days ago
Yveto
• 0
2
votes
1
reply
92
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Sara
• 0
0
votes
5
replies
265
views
ChAMP installation issue
Cha
ChAMP
updated 9 hours ago by
shepherl
3.9k • written 8 days ago by
e1271094
• 0
0
votes
1
reply
169
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 8 days ago by
Guido Hooiveld
★ 4.0k • written 9 days ago by
aogunbaw
• 0
0
votes
2
replies
156
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 7 days ago by
zhouwanding
▴ 10 • written 9 days ago by
Seungmin
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Thank you so much!
Answer: recount3 problem downloading data from source sra
by
Leonardo Collado Torres
★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
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