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4
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28
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
2 hours ago • updated 53 minutes ago
sropri
• 0
0
votes
0
replies
14
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
3 hours ago
Mirella Aurora
• 0
0
votes
0
replies
12
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
4 hours ago
prity6459
• 0
0
votes
1
reply
34
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 hours ago by
Alejandro Reyes
★ 1.9k • written 10 hours ago by
Alessia
• 0
0
votes
1
reply
51
views
Adding columns to DEXSeqResults object
DEXSeq
updated 5 hours ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Clyde
• 0
0
votes
0
replies
16
views
Warning while loading DEP package
DEP
updated 5 hours ago by
shepherl
3.8k • written 5 hours ago by
Namrata
• 0
0
votes
1
reply
36
views
rlog transformation
DESeq2
updated 5 hours ago by
Michael Love
41k • written 11 hours ago by
ishij9717
• 0
0
votes
1
reply
34
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 5 hours ago by
Michael Love
41k • written 12 hours ago by
09191919
• 0
0
votes
1
reply
43
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 hours ago by
Michael Love
41k • written 1 day ago by
ussarizona
• 0
0
votes
1
reply
62
views
covariate with negative and positive values
DESeq2
updated 5 hours ago by
Michael Love
41k • written 1 day ago by
Brynn
• 0
0
votes
1
reply
65
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
0
replies
32
views
Log-cpm values from limma
limma
edgeR
RNASeq
13 hours ago
Shaimaa Gamal
• 0
0
votes
2
replies
69
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 hours ago • updated 1 hour ago
Le
• 0
1
vote
2
replies
68
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago • updated 6 hours ago
Sherin
• 0
0
votes
1
reply
43
views
Input Question for deseq.r
RSeqAn
updated 9 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
Nina
• 0
0
votes
2
replies
103
views
FilterByExpr low counts with small sample size
edgeR
1 day ago • updated 4 hours ago
Jonathan
▴ 10
0
votes
1
reply
43
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 2 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
lonn
• 0
0
votes
6
replies
145
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 22 hours ago by
Gordon Smyth
50k • written 1 day ago by
hortense96
• 0
0
votes
0
replies
26
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News:
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29
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News:
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1 day ago
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0
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41
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
2 days ago
Maliha Tabassum
• 0
0
votes
4
replies
112
views
flowStats Search Error
flowStats
updated 2 days ago by
shepherl
3.8k • written 2 days ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 1 day ago
shepherl
3.8k
0
votes
1
reply
85
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
tian.liu0720
• 0
1
vote
2
replies
70
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
2 days ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
66
views
what is the sampleFiles
chipseq
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
zhulin
• 0
0
votes
1
reply
103
views
Differentially expressed genes in monocle pseudotime
monocle
updated 2 days ago by
Gordon Smyth
50k • written 4 days ago by
kthapa
• 0
4
votes
8
replies
286
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 21 hours ago by
Peter Hickey
▴ 740 • written 7 days ago by
Juan Higareda
• 0
3
votes
3
replies
128
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
6 days ago • updated 12 hours ago
jacques.imbert
• 0
0
votes
1
reply
102
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 2 days ago by
kamryncole1963
• 0 • written 7 days ago by
Sara
• 0
0
votes
3
replies
135
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
55
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
3 days ago
Virangika
• 0
0
votes
0
replies
39
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
3 days ago
Henry
▴ 10
1
vote
1
reply
156
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 3 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
0
votes
3
replies
165
views
DEG with low counts
DESeq2
4 days ago • updated 2 days ago
Rajat
• 0
1
vote
2
replies
215
views
GSVA error
GSVA
4 days ago • updated 3 days ago
Alex
• 0
2
votes
3
replies
228
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
3 days ago • updated 2 days ago
daniel.carbajo
• 0
3
votes
3
replies
254
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 10 days ago by
Netanel
• 0
1
vote
3
replies
295
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 3 days ago by
Gordon Smyth
50k • written 8 days ago by
Simran
• 0
0
votes
1
reply
89
views
Deseq2 Rlog transformation
DESeq2
updated 3 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 0
0
votes
1
reply
663
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 5 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
2
replies
147
views
Design Matrix within group comparison more than two groups
DESeq2
6 days ago • updated 5 days ago
hemantcnaik
• 0
0
votes
6
replies
542
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 6 days ago
shepherl
3.8k
2
votes
2
replies
141
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
6 days ago • updated 5 days ago
julia_mcdonough
• 0
2
votes
2
replies
129
views
[DiffBind] Obtaining normalization factors
DiffBind
6 days ago • updated 2 days ago
Henry
▴ 10
0
votes
1
reply
104
views
Bioinformatics student
Des
DESeq2
updated 6 days ago by
hemantcnaik
• 0 • written 6 days ago by
Sahar
• 0
0
votes
0
replies
61
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
6 days ago
shepherl
3.8k
2
votes
2
replies
129
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
6 days ago • updated 3 days ago
daniel.carbajo
• 0
45,544 results • Page
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Recent ...
Replies
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
sredemption
• 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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3.8k
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