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0
replies
11
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
4 hours ago
Tim Barry
• 0
0
votes
1
reply
35
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
updated 8 hours ago by
James W. MacDonald
66k • written 8 hours ago by
landenshanie
▴ 40
0
votes
2
replies
60
views
How to run allelic imbalance in apeglm
apeglm
updated 11 hours ago by
Michael Love
42k • written 1 day ago by
euge.eugenio
▴ 20
0
votes
1
reply
59
views
ERROR; return code from pthread_create() is 22
affy
updated 13 hours ago by
James W. MacDonald
66k • written 2 days ago by
pickingastar
• 0
0
votes
3
replies
91
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 8 hours ago by
James W. MacDonald
66k • written 1 day ago by
boczniak767
▴ 720
1
vote
1
reply
66
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 13 hours ago by
James W. MacDonald
66k • written 22 hours ago by
ttt
• 0
1
vote
1
reply
47
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 13 hours ago by
James W. MacDonald
66k • written 19 hours ago by
Đình Vinh
• 0
0
votes
0
replies
12
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
13 hours ago
pierre.devillemereuil
• 0
1
vote
2
replies
94
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 14 hours ago
Anna
• 0
0
votes
1
reply
39
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 18 hours ago by
ATpoint
★ 4.1k • written 19 hours ago by
V_Vibes
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
19 hours ago
shahrozimmac
0
0
votes
0
replies
23
views
Processing of curatedmetagenomics
curatedMetagenomicData
1 day ago
Edward
• 0
7
votes
6
replies
637
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
0
votes
5
replies
141
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
1 day ago • updated 15 hours ago
Galina
• 0
0
votes
0
replies
31
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
6
replies
554
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
3 days ago • updated 12 hours ago
Ken C
• 0
2
votes
4
replies
174
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 11 hours ago by
Michael Love
42k • written 3 days ago by
shaunpeterson
• 0
0
votes
0
replies
44
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
2 days ago • updated 1 day ago
Abiologist
• 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
2
replies
122
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
4 days ago
makala
• 0
2
votes
2
replies
401
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
0
votes
0
replies
56
views
determine k during RUVSeq
RUVSeq
RUVnormalize
4 days ago
Ειρήνη
• 0
2
votes
3
replies
124
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
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
83
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
4 days ago
Anton01
• 0
0
votes
0
replies
49
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
225
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
5 days ago • updated 3 days ago
Patadù
▴ 10
0
votes
4
replies
145
views
error running enricher from clusterprofiler
clusterProfiler
cluster
5 days ago
Yael
• 0
2
votes
3
replies
141
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
2
votes
1
reply
88
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
4
votes
9
replies
275
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 4 days ago by
ATpoint
★ 4.1k • written 5 days ago by
pangtaihin
• 0
0
votes
0
replies
44
views
Difference in Contrast in DiffBind
DiffBind
5 days ago
zzrammal
• 0
1
vote
2
replies
112
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
5 days ago
Patadù
▴ 10
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
131
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
0
votes
2
replies
145
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 6 days ago by
zhouwanding
▴ 10 • written 8 days ago by
Seungmin
• 0
1
vote
0
replies
338
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
1
vote
2
replies
138
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago
Daniel
• 0
0
votes
1
reply
104
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
1
vote
0
replies
71
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
6 days ago
Aleena
▴ 30
0
votes
0
replies
61
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
6 days ago
Researcher
• 0
0
votes
8
replies
522
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
1
vote
3
replies
260
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
3
votes
4
replies
293
views
Store output of matchPWM()
biostrings
Biostrings
19 days ago • updated 7 days ago
mat149
▴ 70
1
vote
2
replies
256
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
2
replies
110
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
7 days ago • updated 6 days ago
Yveto
• 0
0
votes
1
reply
156
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 7 days ago by
Guido Hooiveld
★ 4.0k • written 8 days ago by
aogunbaw
• 0
0
votes
3
replies
193
views
ChAMP installation issue
Cha
ChAMP
8 days ago • updated 6 days ago
e1271094
• 0
45,680 results • Page
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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.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
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
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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