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0
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39
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
3 days ago
Henry
▴ 10
1
vote
2
replies
214
views
GSVA error
GSVA
4 days ago • updated 3 days ago
Alex
• 0
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
1
reply
89
views
Deseq2 Rlog transformation
DESeq2
updated 3 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 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
3
votes
3
replies
253
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 10 days ago by
Netanel
• 0
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
0
votes
1
reply
108
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 8 days ago by
Lucie
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 4 days ago by
Samuel Ahuno
• 0 • written 7.9 years ago by
maltethodberg
▴ 170
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
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 5 days ago by
gptnederlands.nl
• 0 • written 13 months ago by
Wolfgang Huber
★ 13k
5
votes
6
replies
372
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 days ago by
ATpoint
★ 4.0k • written 9 days ago by
nhaus
▴ 30
6
votes
8
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 5 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
2
votes
2
replies
140
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
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
3
votes
1
reply
731
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.1 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
6
replies
541
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
335
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
7 days ago • updated 6 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
60
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
6 days ago
shepherl
3.8k
0
votes
0
replies
67
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
6 days ago
Stevie Pederson
• 0
0
votes
1
reply
140
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
0
votes
4
replies
178
views
Storing directories inside an ExperimentHub package?
ExperimentHub
8 days ago • updated 7 days ago
Tim Barry
• 0
8
votes
23
replies
749
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 7 days ago by
Robert Castelo
★ 3.2k • written 8 days ago by
Bine
▴ 40
3
votes
6
replies
201
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
7 days ago
nhaus
▴ 30
0
votes
0
replies
70
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
7 days ago
communication
• 0
0
votes
6
replies
282
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 7 days ago by
Tim Peters
▴ 170 • written 16 days ago by
s.malik
• 0
0
votes
0
replies
99
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
8 days ago
Eryn
• 0
0
votes
0
replies
67
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
8 days ago
Dennis
• 0
1
vote
6
replies
426
views
GSVA on separate healthy and disease datasets
GSVA
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
Lucy
▴ 60
0
votes
1
reply
313
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 8 days ago by
Lluís Revilla Sancho
▴ 730 • written 6 months ago by
karmasstark
• 0
0
votes
1
reply
103
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 8 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Merav
• 0
0
votes
0
replies
80
views
ggtree tip label position (depth)
ggtree
9 days ago • updated 8 days ago
Roope
• 0
0
votes
2
replies
177
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
41k • written 13 days ago by
nhaus
▴ 30
0
votes
1
reply
126
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 8 days ago by
Michael Love
41k • written 9 days ago by
Adelaide
• 0
0
votes
2
replies
212
views
Regressing out batch effects
DESeq2
updated 8 days ago by
Michael Love
41k • written 14 days ago by
kys91240
• 0
0
votes
1
reply
120
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
zh9118
• 0
1
vote
10
replies
377
views
Obtaining pheno data from CEL files
GEO
affy
16 days ago • updated 9 days ago
Kurtis
• 0
0
votes
1
reply
485
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 9 days ago by
ivorychan7777
• 0 • written 14 months ago by
609b0d25
• 0
0
votes
1
reply
193
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
updated 9 days ago by
Wei Shi
★ 3.6k • written 18 days ago by
isaac.vock
• 0
2
votes
6
replies
303
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
10 days ago
Chris
• 0
0
votes
1
reply
145
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
BCS12
• 0
0
votes
0
replies
100
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
10 days ago
arne.sahm
• 0
0
votes
0
replies
71
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
10 days ago
Wolfgang Huber
★ 13k
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 days ago • updated 10 days ago
Chris
• 0
0
votes
4
replies
279
views
Help with design.matrix
limma
13 days ago • updated 12 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
136
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 12 days ago by
Gordon Smyth
50k • written 12 days ago by
avery
• 0
1
vote
3
replies
218
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
106
views
Granges regionCounts not returning the expected number of entries
methylKit
13 days ago
Modoc Kesner
▴ 10
1
vote
2
replies
188
views
MethylKit read issue
methylKit
updated 13 days ago by
James W. MacDonald
65k • written 18 days ago by
CHEN
• 0
45,544 results • Page
2 of 911
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Replies
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…
Answer: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
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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