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0
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0
replies
11
views
BiocNeighbours Utility for k-Nearest Neighbour Classification
Classification
BiocNeighbors
4 hours ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
69
views
Handling Epic Array Data
minfi
8 hours ago • updated 5 hours ago
Melisa Tecik
• 0
0
votes
2
replies
143
views
Allele frequencies for ALL alleles of one SNP ?
Bioconductor
updated 11 hours ago by
Robert Castelo
★ 3.4k • written 6 days ago by
Abiologist
• 0
2
votes
2
replies
137
views
preprocessIllumina error with EPICv2 array
minfi
EPICv2manifest
1 day ago • updated 11 hours ago
Rakesh
• 0
0
votes
2
replies
99
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
1 day ago • updated 11 hours ago
giulia.gentile
• 0
0
votes
3
replies
81
views
CleanUpRNAseq with a GTF that is missing mitochondria annotation data
CleanUpRNAseq
updated 11 hours ago by
Haibo Liu
• 0 • written 1 day ago by
rcreed
• 0
1
vote
1
reply
64
views
UniProt.ws query loading indefinitely
UniProt.ws
updated 13 hours ago by
James W. MacDonald
67k • written 14 hours ago by
Patrick
• 0
0
votes
2
replies
66
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 1 day ago by
Kent
• 0
0
votes
2
replies
104
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker
GenomicScores
phastCons100way.UCSC.hg38
GenomicFeatures
updated 17 hours ago by
Robert Castelo
★ 3.4k • written 3 days ago by
rania.alanany
• 0
0
votes
2
replies
113
views
Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
updated 19 hours ago by
Gordon Smyth
51k • written 1 day ago by
Jonathan
• 0
3
votes
2
replies
210
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 23 hours ago by
Gordon Smyth
51k • written 1 day ago by
Ahdee
▴ 50
1
vote
5
replies
224
views
Package needs internet access
BSgenome
BSgenome.Hsapiens.UCSC.hg38
Offline
updated 13 hours ago by
James W. MacDonald
67k • written 1 day ago by
firestar
▴ 20
0
votes
2
replies
86
views
Limma Interaction Effect with Covariates
limma
DMRcate
1 day ago
kitzhu
• 0
0
votes
1
reply
51
views
Using Affymetrix Custom Array
ArrayExpress
makecdfenv
AffymetrixChip
gcrma
GeneExpression
updated 1 day ago by
James W. MacDonald
67k • written 1 day ago by
Piotr.Keller
• 0
1
vote
2
replies
152
views
Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 1 day ago by
James W. MacDonald
67k • written 1 day ago by
Dhite
• 0
0
votes
1
reply
55
views
eRNAs count
RNASeq
DESeq2
updated 1 day ago by
ATpoint
★ 4.5k • written 1 day ago by
Irene
• 0
0
votes
0
replies
31
views
Job:
Postdoctoral position in Computational Epigenomics of Aging and Cancer
Aging
Epigenetics
JobPosting
Postdoctor
Cancer
2 days ago
xiaolong
• 0
0
votes
1
reply
316
views
DESeq2 rerun returns different results
DESeq2
updated 4 days ago by
ATpoint
★ 4.5k • written 5 days ago by
wl1111
• 0
2
votes
3
replies
773
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 2 days ago by
Gordon Smyth
51k • written 6 days ago by
kyj2226
• 0
0
votes
1
reply
163
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 5 days ago by
Michael Love
42k • written 6 days ago by
Jason
• 0
6
votes
6
replies
3.8k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.6 years ago by
Colari19
▴ 60
0
votes
0
replies
83
views
WGCNA module preservation using only adjacency matrix
WGCNA
6 days ago
yang1641
• 0
0
votes
0
replies
35
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
6 days ago
Simone
• 0
0
votes
4
replies
369
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
6 days ago
dseauer
• 0
0
votes
2
replies
235
views
installation error for BiocNeighbors package
BiocNeighbors
6 days ago
育
• 0
0
votes
2
replies
263
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
8 days ago • updated 6 days ago
Stefano Mangiola
▴ 20
0
votes
1
reply
129
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 7 days ago by
Guido Hooiveld
★ 4.1k • written 7 days ago by
Najla Abassi
• 0
2
votes
2
replies
509
views
Handling biological replicates in DESeq2
DESeq2
updated 7 days ago by
ATpoint
★ 4.5k • written 8 days ago by
sk
• 0
0
votes
0
replies
78
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP
ChAMPdata
8 days ago
elgomez
• 0
0
votes
1
reply
183
views
forgeBSgenomeDataPkgFromNCBI: Error in find_NCBI_assembly_ftp_dir unable to find FTP dir
BSgenomeForge
non-modelorganism
unabletofindFTPdir
updated 8 days ago by
Hervé Pagès
16k • written 8 days ago by
Geetha
• 0
0
votes
3
replies
387
views
ChIPpeakAnno can not load data
genomes
ChIPpeakAnno
written 9 weeks ago by
文杰
• 0
10
votes
7
replies
1.7k
views
Why in Bioconductor community people rarely upvote questions?
bioconductor
updated 8 days ago by
shepherl
4.1k • written 21 months ago by
L
▴ 50
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 5.9 years ago by
aishu.jp
▴ 30
0
votes
1
reply
156
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
11 days ago • updated 5 days ago
abadgerw
• 0
0
votes
1
reply
264
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
11 days ago • updated 5 days ago
abadgerw
• 0
1
vote
6
replies
854
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 11 days ago by
Michael Love
42k • written 11 days ago by
nramakr
▴ 10
2
votes
4
replies
1.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR
BatchEffect
updated 8 days ago by
Gordon Smyth
51k • written 12 days ago by
Thili
• 0
1
vote
8
replies
957
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 15 days ago by
Adam Marstrand
• 0
0
votes
2
replies
313
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 13 days ago by
ballackselma
• 0
2
votes
7
replies
959
views
Annotation for EPICv2
EpicV2
ChAMPdata
updated 14 days ago by
icecreamlover
• 0 • written 6 weeks ago by
nurkenber
• 0
0
votes
0
replies
107
views
ChIP peaks comparison
ChIPSeqData
genomes
ChIPSeq
14 days ago
user_bioinfo
• 0
0
votes
2
replies
666
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi
GOstats
14 days ago • updated 12 days ago
GV Yoshikawa
• 0
1
vote
2
replies
866
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
15 days ago • updated 14 days ago
Ai
• 0
4
votes
5
replies
556
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
15 days ago • updated 14 days ago
LuciaNhu
• 0
0
votes
0
replies
106
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
15 days ago
kim
• 0
0
votes
0
replies
99
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
15 days ago
daccar98
• 0
0
votes
0
replies
117
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
15 days ago
brayas13
• 0
2
votes
3
replies
652
views
featureCounts segmentation fault with large chromosomes
Rsubread
28 days ago • updated 16 days ago
vkkodali
▴ 10
0
votes
1
reply
350
views
Average expression of genes across replicates
DESeq2
updated 16 days ago by
ATpoint
★ 4.5k • written 18 days ago by
James
• 0
0
votes
1
reply
330
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 16 days ago by
ATpoint
★ 4.5k • written 18 days ago by
Katerina
• 0
46,184 results • Page
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Replies
Comment: Handling Epic Array Data
by
Melisa Tecik
• 0
Thank you so much for the clarification. As you said the replicates are the cells from different plates. For instance, both R01C01 and R05C…
Answer: Handling Epic Array Data
by
James W. MacDonald
67k
You don't need a sample sheet. It is just a simple way to identify the Idat files and possibly include sample information. But you appear t…
Comment: preprocessIllumina error with EPICv2 array
by
Rakesh
• 0
Amazing, thanks for the help!
Answer: Allele frequencies for ALL alleles of one SNP ?
by
Robert Castelo
★ 3.4k
Hi, the [GenomicScores](https://bioconductor.org/packages/GenomicSCores) package provides supporting infrastructure to create annotation re…
Answer: preprocessIllumina error with EPICv2 array
by
James W. MacDonald
67k
You shouldn't need to change the annotation, and certainly not like that. You should never need to use the `@` function directly - there ar…
Votes
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: preprocessIllumina error with EPICv2 array
Answer: preprocessIllumina error with EPICv2 array
Answer: UniProt.ws query loading indefinitely
Answer: Package needs internet access
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