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0
votes
0
replies
19
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
11 hours ago
Tim Barry
• 0
0
votes
2
replies
47
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
updated 1 hour ago by
blackwidowzzz
• 0 • written 15 hours ago by
landenshanie
▴ 40
0
votes
0
replies
13
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
20 hours ago
pierre.devillemereuil
• 0
0
votes
1
reply
40
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
53
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 20 hours 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
133
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 20 hours ago by
James W. MacDonald
66k • written 1 day ago by
ttt
• 0
0
votes
0
replies
24
views
Processing of curatedmetagenomics
curatedMetagenomicData
1 day ago
Edward
• 0
1
vote
3
replies
100
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 15 hours ago by
James W. MacDonald
66k • written 1 day ago by
boczniak767
▴ 720
0
votes
2
replies
66
views
How to run allelic imbalance in apeglm
apeglm
updated 18 hours ago by
Michael Love
42k • written 1 day ago by
euge.eugenio
▴ 20
0
votes
0
replies
32
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
1 day ago
Bibi
• 0
0
votes
5
replies
146
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
2 days ago • updated 22 hours ago
Galina
• 0
1
vote
2
replies
95
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 20 hours ago
Anna
• 0
0
votes
1
reply
61
views
ERROR; return code from pthread_create() is 22
affy
updated 19 hours ago by
James W. MacDonald
66k • written 2 days ago by
pickingastar
• 0
0
votes
0
replies
45
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
180
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 18 hours ago by
Michael Love
42k • written 3 days ago by
shaunpeterson
• 0
0
votes
3
replies
116
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 3 days ago by
damian.szk
▴ 80 • written 3 days ago by
ninidea
• 0
0
votes
6
replies
554
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 18 hours ago
Ken C
• 0
0
votes
2
replies
125
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
4 days ago
makala
• 0
0
votes
0
replies
58
views
determine k during RUVSeq
RUVSeq
RUVnormalize
4 days ago
Ειρήνη
• 0
0
votes
0
replies
59
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
4 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
15
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
4 days ago
oliverelijhan
0
0
votes
0
replies
87
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
5 days ago
Anton01
• 0
2
votes
3
replies
129
views
Problem installing ChAMP on a MacBook
ChAMP
updated 4 days ago by
shepherl
3.9k • written 5 days ago by
Galia
• 0
0
votes
0
replies
53
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
5 days ago
danalvoronov
▴ 10
0
votes
0
replies
52
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
5 days ago
k200987
• 0
2
votes
5
replies
228
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
5 days ago • updated 4 days ago
Patadù
▴ 10
0
votes
4
replies
149
views
error running enricher from clusterprofiler
clusterProfiler
cluster
5 days ago
Yael
• 0
2
votes
3
replies
148
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
Guillermo
• 0
0
votes
0
replies
45
views
Difference in Contrast in DiffBind
DiffBind
6 days ago
zzrammal
• 0
4
votes
9
replies
282
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 4 days ago by
ATpoint
★ 4.1k • written 6 days ago by
pangtaihin
• 0
1
vote
2
replies
115
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
6 days ago • updated 5 days ago
Patadù
▴ 10
0
votes
3
replies
135
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 5 days ago by
Michael Love
42k • written 6 days ago by
Kasper
• 0
1
vote
2
replies
139
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago
Daniel
• 0
1
vote
3
replies
261
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Ashley
• 0
1
vote
2
replies
257
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
7 days ago • updated 4 days ago
BioinfGuru
▴ 30
0
votes
8
replies
528
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 6 days ago by
BioinfGuru
▴ 30 • written 7 days ago by
Eric Katagirya
• 0
0
votes
1
reply
105
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 6 days ago by
Michael Love
42k • written 7 days ago by
piemmea
• 0
0
votes
2
replies
112
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
7 days ago • updated 6 days ago
Yveto
• 0
2
votes
1
reply
89
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Sara
• 0
0
votes
2
replies
148
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 6 days ago by
zhouwanding
▴ 10 • written 8 days ago by
Seungmin
• 0
2
votes
2
replies
406
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
9 days ago • updated 4 days ago
Matthew Thornton
▴ 360
4
votes
5
replies
343
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
15 days ago • updated 5 days ago
Chris
▴ 10
7
votes
6
replies
641
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 15 days ago by
robersy
• 0
1
vote
2
replies
208
views
Citation for edgeR user guide
edgeR
written 27 days ago by
k___
▴ 30
1
vote
0
replies
339
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 6 days ago
shepherl
3.9k
0
votes
2
replies
755
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 5 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 6 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
2
replies
959
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 4 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
55 results • Page
1 of 2
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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