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questions
0
votes
0
replies
233
views
How to highlight specific portion of the gene and its isoform using ggbio
ggbio
isoform
r
3 months ago by
camillab.
▴ 160
1
vote
10
replies
962
views
Error getting the genome on clinvaR
genome
r
clinvaR
3 months ago by
camillab.
▴ 160
1
vote
2
replies
415
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 5 months ago by
Jeremy
▴ 910 • written 5 months ago by
camillab.
▴ 160
2
votes
4
replies
877
views
How to 'organize' multiple umap/genes generates with Seurat `FeaturePlot`in a specific way
R
FeaturePlot
Umap
Seurat
updated 6 months ago by
LauferVA
4.2k • written 6 months ago by
camillab.
▴ 160
1
vote
2
replies
943
views
How to remove the default title to a DimPlot() splitted into two by group.by ?
Dimplot
title
Seurat
6 months ago by
camillab.
▴ 160
1
vote
2
replies
1.4k
views
Seurat changing order cluster shown in the violin plot
R
violin
Seurat
6 months ago by
camillab.
▴ 160
3
votes
6
replies
788
views
Exporting DEGs obtained from DESeq2
R
Deseq2
updated 7 months ago by
Ram
43k • written 7 months ago by
camillab.
▴ 160
4
votes
6
replies
843
views
identify DEGs across all conditions and per specific conditions
R
DEseq2
updated 7 months ago by
Yogi
▴ 70 • written 7 months ago by
camillab.
▴ 160
1
vote
5
replies
737
views
CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
R
Picard
CollectRnaSeqMetrics
updated 7 months ago by
Ram
43k • written 7 months ago by
camillab.
▴ 160
2
votes
4
replies
1.1k
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
7 months ago by
camillab.
▴ 160
5
votes
7
replies
956
views
Salmon index not progressing
salmon
updated 7 months ago by
Michael
54k • written 7 months ago by
camillab.
▴ 160
3
votes
10
replies
1.2k
views
STAR index not working
STAR
RNA-Seq
7 months ago by
camillab.
▴ 160
1
vote
3
replies
600
views
Fastqc loop
fastQC
r
RNA-seq
7 months ago by
camillab.
▴ 160
1
vote
3
replies
601
views
Theoretical question about scRNA-seq
R
scRNA-seq
updated 8 months ago by
dsull
★ 5.9k • written 8 months ago by
camillab.
▴ 160
1
vote
2
replies
557
views
How ti identify genes per terms in with topGO for scRNAseq dataset
scRNAseq
r
GSEA
topGO
8 months ago by
camillab.
▴ 160
0
votes
0
replies
339
views
Enrichment analysis on scRNSseq on which genes/clusters perform ReactomeGSA and GSEA?
ReactomeGSA
r
integration
scRNAseq
GSA
9 months ago by
camillab.
▴ 160
2
votes
1
reply
812
views
How to specify which resolution I want to be plotted in the UMAP?
resolution
scRNSeq
harmony
R
map
updated 9 months ago by
Basti
★ 2.0k • written 9 months ago by
camillab.
▴ 160
3
votes
3
replies
1.5k
views
Leiden algorithm not working R studio scRNAseq
scRNAseq
R
leidenAlg
reticulate
updated 9 months ago by
jared.andrews07
★ 16k • written 9 months ago by
camillab.
▴ 160
0
votes
2
replies
488
views
scRNAseq: integration downstream analysis and identification genes altered in one condition
scRNAseq
R
integration
updated 9 months ago by
Ram
43k • written 9 months ago by
camillab.
▴ 160
6
votes
2
replies
650
views
scRNAseq error source a custom function
R
scRNA-seq
updated 9 months ago by
Hamid Ghaedi
3.2k • written 9 months ago by
camillab.
▴ 160
3
votes
6
replies
1.1k
views
How to get information about promoter from bulk-RNAseq?
promoter
R
RNA-seq
updated 10 months ago by
rfran010
▴ 900 • written 10 months ago by
camillab.
▴ 160
8
votes
4
replies
1.0k
views
R ggrepel for overlapping text in the whole plot
overlapping
r
ggrepel
ggplot
updated 12 months ago by
Trivas
★ 1.7k • written 12 months ago by
camillab.
▴ 160
9
votes
5
replies
1.2k
views
6 follow
ORA analysis (over-representation analysis) : different package different padjusted and qvalue
r
p-value
ORA
q-value
updated 12 months ago by
love-bioinfo
▴ 20 • written 13 months ago by
camillab.
▴ 160
4
votes
2
replies
1.4k
views
specificy ggrepel which genes not overlap in a scatterplot
R
ggplot2
ggrepel
updated 2.0 years ago by
Matthias Zepper
4.6k • written 2.0 years ago by
camillab.
▴ 160
1
vote
2
replies
882
views
Plot genes derived from time course experiment as line graph
line
RNAseq
ggplot
R
updated 2.5 years ago by
gglim
▴ 140 • written 2.6 years ago by
camillab.
▴ 160
0
votes
6
replies
6.8k
views
How to change the default font in ggplot 2
font
ggplot2
Arial
2.7 years ago by
camillab.
▴ 160
4
votes
3
replies
1.6k
views
Scatterplot ggplot: too many overlapping point make an area magnified/ increase specific areas
overlapping
ggplot
scatterplot
r
updated 3.0 years ago by
cpad0112
21k • written 3.0 years ago by
camillab.
▴ 160
5
votes
8
replies
1.9k
views
Loading PCA - different value depending on the package used
factormineR
PCAtools
pca
prcomp
loadings
updated 3.0 years ago by
Kevin Blighe
87k • written 3.0 years ago by
camillab.
▴ 160
1
vote
1
reply
1.2k
views
Reactome website gene expression analysis
gene_expression_analysis_tool
Reactome_website
updated 3.0 years ago by
GenoMax
141k • written 3.0 years ago by
camillab.
▴ 160
3
votes
6
replies
1.5k
views
Covariate correction which data take for downstream analysis?
R
linear-regression
residual
fitted-values
updated 2.5 years ago by
fr
▴ 210 • written 3.1 years ago by
camillab.
▴ 160
3
votes
3
replies
3.2k
views
Error in y - mu : non-numeric argument to binary operator - linear regression loop
bulkRNAseq
R
linear
regression
updated 3.2 years ago by
Sam
★ 4.7k • written 3.2 years ago by
camillab.
▴ 160
3
votes
1
reply
1.5k
views
Error on Linear regression bulkRNAseq
R
linear
regression
residue
updated 3.2 years ago by
rpolicastro
13k • written 3.2 years ago by
camillab.
▴ 160
2
votes
3
replies
1.2k
views
NO FDR <0.05 in the whole dataset
R
RNA-Seq
FDR
qvalue
updated 3.2 years ago by
rpolicastro
13k • written 3.2 years ago by
camillab.
▴ 160
4
votes
9
replies
7.9k
views
p.adjusted p value
r
pvalue
FDR
RNA-Seq
updated 3.2 years ago by
ATpoint
82k • written 3.2 years ago by
camillab.
▴ 160
1
vote
8
replies
1.0k
views
PCA - untreated sample cluster separated
R
bulk-RNAseq
PCA
variability
3.2 years ago by
camillab.
▴ 160
13
votes
13
replies
65k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R
RNA-Seq
pheatmap
arg10
updated 3.3 years ago by
henry-keen
▴ 40 • written 3.8 years ago by
camillab.
▴ 160
3
votes
6
replies
1.3k
views
Volcano plot with highlighted significantly up/down regulated genes with specific normalised reads value?
R
RNA-Seq
EnhancedVolcano
plot
3.5 years ago by
camillab.
▴ 160
4
votes
1
reply
2.8k
views
Gene enrichment analysis clusterProfiler
RNA-Seq
R
clusterProfiler
GSEA
updated 3.5 years ago by
Hannes
▴ 50 • written 3.6 years ago by
camillab.
▴ 160
1
vote
8
replies
984
views
Big dataset how to plot gene expression differences?
R
plot
dataset
3.5 years ago by
camillab.
▴ 160
3
votes
10
replies
1.6k
views
How to identify which genes are responsible for the different cluster without PCA
R
hclust
clustering
bulkRNAseq
updated 3.5 years ago by
Friederike
8.9k • written 3.5 years ago by
camillab.
▴ 160
1
vote
0
replies
953
views
Average Spearman's correlation: how to calculate/find it?
R
spearman
correlation
average
3.5 years ago by
camillab.
▴ 160
1
vote
1
reply
9.5k
views
basic barplot with ggplot: assign specific color to column with specific values
R
ggplot
barplot
updated 3.6 years ago by
rpolicastro
13k • written 3.6 years ago by
camillab.
▴ 160
7
votes
5
replies
1.4k
views
How to convert gallus gallus entrezID into human entrezID
R
RNA-Seq
entrezID
reactome
updated 3.6 years ago by
zx8754
11k • written 3.6 years ago by
camillab.
▴ 160
3
votes
10
replies
1.6k
views
PCA and loadings: how to discriminate betwen real and background/noise signal?
PCA
PCAtools
loadings
RNA-Seq
R
3.7 years ago by
camillab.
▴ 160
2
votes
5
replies
1.4k
views
PCA and loadings question
bulkRNA
PCA
loadings
scale
updated 3.7 years ago by
Biostar
20 • written 3.8 years ago by
camillab.
▴ 160
1
vote
4
replies
1.1k
views
Decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort
decreasing
R
RNA-Seq
updated 3.7 years ago by
Ram
43k • written 3.7 years ago by
camillab.
▴ 160
1
vote
3
replies
1.5k
views
PCA loadings/roation : different variables depending on the code
RNA-Seq
PCA
prcomp
FactoMineR
loading
updated 3.7 years ago by
Kevin Blighe
87k • written 3.7 years ago by
camillab.
▴ 160
13
votes
12
replies
2.7k
views
zScore conversion: zFPKM vs scale function
RNA-Seq
zscores
zFPKM
scale
updated 3.8 years ago by
A. Domingues
★ 2.7k • written 3.8 years ago by
camillab.
▴ 160
3
votes
5
replies
3.1k
views
PCA trasformation on Z scored data
bulkRNAseq
PCA
scale
logTRANSFORM
updated 3.8 years ago by
Kevin Blighe
87k • written 3.8 years ago by
camillab.
▴ 160
3
votes
6
replies
4.5k
views
Heatmap on Z scores data: scale or not?
heatmap
RNA-Seq
Zscores
updated 3.8 years ago by
Shalu Jhanwar
▴ 520 • written 3.8 years ago by
camillab.
▴ 160
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