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0
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5
replies
1.6k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
107
views
Differentially expressed genes in monocle pseudotime
monocle
updated 3 days ago by
Gordon Smyth
50k • written 5 days ago by
kthapa
• 0
2
votes
2
replies
133
views
[DiffBind] Obtaining normalization factors
DiffBind
6 days ago • updated 3 days ago
Henry
▴ 10
2
votes
3
replies
245
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 days ago • updated 3 days ago
daniel.carbajo
• 0
0
votes
1
reply
107
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 3 days ago by
kamryncole1963
• 0 • written 8 days ago by
Sara
• 0
0
votes
4
replies
2.7k
views
SingleR Label.Ont
SingleR
updated 3 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
0
replies
59
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
3 days ago
Virangika
• 0
0
votes
0
replies
43
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
3 days ago
Henry
▴ 10
1
vote
2
replies
224
views
GSVA error
GSVA
5 days ago • updated 3 days ago
Alex
• 0
1
vote
1
reply
160
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 4 days ago by
Michael Love
41k • written 8 days ago by
Weiqian
▴ 10
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
1
vote
3
replies
303
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
3
votes
3
replies
258
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 11 days ago by
Netanel
• 0
2
votes
2
replies
132
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
7 days ago • updated 4 days ago
daniel.carbajo
• 0
0
votes
1
reply
110
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 5 days ago by
Samuel Ahuno
• 0 • written 7.9 years ago by
maltethodberg
▴ 170
1
vote
2
replies
152
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 6 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
6
replies
377
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.0k • written 9 days ago by
nhaus
▴ 30
2
votes
2
replies
148
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
6 days ago
julia_mcdonough
• 0
0
votes
1
reply
667
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
3
votes
1
reply
733
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
544
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
336
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
109
views
Bioinformatics student
Des
DESeq2
updated 6 days ago by
hemantcnaik
• 0 • written 6 days ago by
Sahar
• 0
0
votes
0
replies
64
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
6 days ago
shepherl
3.8k
0
votes
0
replies
68
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
7 days ago
Stevie Pederson
• 0
0
votes
1
reply
141
views
DESeq2 gives an error and R crashes
DESeq2
8 days ago • updated 7 days ago
Shefali
• 0
0
votes
4
replies
180
views
Storing directories inside an ExperimentHub package?
ExperimentHub
8 days ago • updated 7 days ago
Tim Barry
• 0
8
votes
23
replies
763
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
206
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
8 days ago • updated 7 days ago
nhaus
▴ 30
0
votes
0
replies
73
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
288
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 8 days ago by
Tim Peters
▴ 170 • written 16 days ago by
s.malik
• 0
0
votes
0
replies
100
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
8 days ago
Eryn
• 0
0
votes
0
replies
68
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
8 days ago
Dennis
• 0
1
vote
6
replies
427
views
GSVA on separate healthy and disease datasets
GSVA
updated 8 days ago by
James W. MacDonald
65k • written 10 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
106
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
81
views
ggtree tip label position (depth)
ggtree
9 days ago
Roope
• 0
0
votes
2
replies
179
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 9 days ago by
Michael Love
41k • written 14 days ago by
nhaus
▴ 30
0
votes
1
reply
128
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
Adelaide
• 0
0
votes
2
replies
214
views
Regressing out batch effects
DESeq2
updated 9 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
381
views
Obtaining pheno data from CEL files
GEO
affy
16 days ago • updated 10 days ago
Kurtis
• 0
0
votes
1
reply
486
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 10 days ago by
ivorychan7777
• 0 • written 14 months ago by
609b0d25
• 0
0
votes
1
reply
195
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
updated 10 days ago by
Wei Shi
★ 3.6k • written 18 days ago by
isaac.vock
• 0
2
votes
6
replies
308
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
146
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
103
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
10 days ago
arne.sahm
• 0
0
votes
0
replies
73
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
11 days ago
Wolfgang Huber
★ 13k
200 results • Page
2 of 4
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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