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Showing top results for tag:
R
•
reset
1
vote
1
reply
107
views
Using NumReads column of quants.genes.sf file to build DESeq2 input
R
deseq2
rna-seq
salmon
updated 16 hours ago by
i.sudbery
20k • written 17 hours ago by
Ezequiel
▴ 10
0
votes
1
reply
99
views
SCE object acting strangley
SCE
R
Seurat
object
SingleCellExperiment
updated 19 hours ago by
ATpoint
85k • written 20 hours ago by
wykpenguin
• 0
0
votes
2
replies
177
views
R encountering fatal error and quitting the session
R
randomForestSRC
Random-forest
16 hours ago by
anjalivasudevan98
▴ 40
3
votes
3
replies
208
views
IDAT to FASTA workflow
PLINK
R
IDAT
FASTA
GWAS
updated 1 day ago by
GenoMax
146k • written 1 day ago by
sabrilo171
▴ 10
9
votes
5
replies
26k
views
PC3 & PC2 using plotPCA function in R
R
plotPCA
PCA
updated 1 day ago by
Ram
44k • written 7.6 years ago by
User000
▴ 710
0
votes
1
reply
149
views
Plot query cells on top of reference cells in UMAP
R
Integration
Seurat
updated 2 days ago by
Bastien Hervé
5.8k • written 3 days ago by
saicchan
• 0
0
votes
2
replies
235
views
Comparing GSEA mutant data to wild type
python
gene
GSEA
R
7 hours ago by
conmul
• 0
0
votes
0
replies
125
views
Duplicates in TCGAanalyze_Normalization
R
TCGAanalyze_Normalization
TCGAbiolinks
studio
4 days ago by
Azra
▴ 10
5
votes
3
replies
386
views
Selecting DEGs for gene ontology using clusterprofiler and DESeq2
R
DESeq2
RNAseq
3 days ago by
a.basitkhan1990
▴ 60
1
vote
2
replies
297
views
getMappedEntrezIDs from missmethyl package R
R
missmethyl
CpG
methylation
gene
6 days ago by
Rut_MDLV
• 0
0
votes
2
replies
271
views
News:
Course on Reproducibility Data Analysis with R
R
Github
Git
Reproducibility
Docker
7 days ago by
carlopecoraro2
★ 2.6k
1
vote
1
reply
339
views
WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendrogram?
R
genes
transcriptomics
WGCNA
updated 15 hours ago by
allingt
• 0 • written 8 days ago by
shubhankarpawar3
▴ 10
0
votes
0
replies
140
views
How to normalise multiple datasets together using GEO2R?
geo
R
normalisation
geo2r
microarray
9 days ago by
Sai
• 0
1
vote
5
replies
405
views
gene ID to gene symbol in R
R
updated 9 days ago by
Gordon Smyth
★ 7.5k • written 9 days ago by
pinheirofabiano
▴ 90
0
votes
3
replies
269
views
Error in as.unit(e2) : object is not coercible to a unit
R
Venn-diagram
venn
updated 8 days ago by
Ram
44k • written 9 days ago by
otieno43
▴ 30
2
votes
2
replies
232
views
Highly skewed distribution of differentially expressed (DE) genes
R
RNAseq
Deseq2
updated 9 days ago by
LChart
4.3k • written 9 days ago by
Maria
• 0
0
votes
1
reply
955
views
Using TCGABioLinks to query multiple cancer studies
RNA-Seq
R
TCGA
updated 10 days ago by
GenoMax
146k • written 3.8 years ago by
ivykosater
• 0
0
votes
0
replies
120
views
How to obtain level 2 GO term from go_id?
R
GO-term
11 days ago by
Chenfeng
• 0
2
votes
0
replies
144
views
Blog:
How Seurat PCA projection, KNN and MNN for label transfer work
R
RNA-seq
scRNA-seq
PCA
updated 10 days ago by
Ram
44k • written 11 days ago by
Ming Tommy Tang
★ 4.4k
0
votes
1
reply
194
views
Rnbeads
Rnbeads
methylation
DNA
R
updated 13 days ago by
Ram
44k • written 13 days ago by
AJ
• 0
0
votes
0
replies
87
views
GWAS() function error rrBLUP package for GWAS
R
Rstudio
rrBLUP
GWAS
updated 14 days ago by
Ram
44k • written 14 days ago by
giulia.trauzzi
▴ 30
1
vote
4
replies
377
views
Issues with pGIG : Negative probability and unexpected P value order
R
distribution
gamlss
fitting
14 days ago by
jayeshkumarsundaram
• 0
1
vote
6
replies
333
views
0-based or 1-based file format using R pipeline?
1-based
0-based
r
updated 15 days ago by
Ram
44k • written 16 days ago by
Nur
• 0
0
votes
0
replies
122
views
News:
Course - Introduction to the Analysis of Longitudinal Data in Biology Using R
Longitudinal-Data
R
Epidemiology
Forecasting
Gene-Expression
updated 16 days ago by
Ram
44k • written 16 days ago by
carlopecoraro2
★ 2.6k
0
votes
1
reply
166
views
Seurat Xenium QC
R
Xenium
spatial
Seurat
updated 17 days ago by
Bastien Hervé
5.8k • written 17 days ago by
yura.grabovska
▴ 600
3
votes
4
replies
365
views
What is wrong with my scripts?
R
GDC
TCGAbiolinks
Bioconductor
updated 17 days ago by
Ming Tommy Tang
★ 4.4k • written 17 days ago by
nuorain
▴ 30
3
votes
2
replies
297
views
cnv_facets run problem
R
cnv_facets
17 days ago by
hamideh
▴ 20
0
votes
0
replies
142
views
News:
Genomic Data Visualisation in R (online course)
Data-Visualisation
Genomic-Data
R
17 days ago by
carlopecoraro2
★ 2.6k
2
votes
4
replies
436
views
Boxplot with adjustment for variable
R
boxplot
updated 17 days ago by
zx8754
12k • written 20 days ago by
Bine
▴ 70
3
votes
9
replies
769
views
I need help with this R script. Thanks.
R
updated 17 days ago by
Ram
44k • written 20 days ago by
nuorain
▴ 30
2
votes
2
replies
360
views
Can anyone share with me the R code for GSEA analysis?
R
code
GSEA
updated 21 days ago by
GenoMax
146k • written 21 days ago by
nuorain
▴ 30
1
vote
2
replies
339
views
DESeq2: adjusted p-values become NA when sub-setting samples
R
DEG
RNA-seq
DESeq2
updated 21 days ago by
GenoMax
146k • written 21 days ago by
txema.heredia
▴ 190
2
votes
3
replies
323
views
Removing features from RNA assay in seurat
R
SEURAT
sc-RNA-Seq
updated 22 days ago by
yura.grabovska
▴ 600 • written 22 days ago by
Varun Gupta
★ 1.3k
5
votes
3
replies
362
views
creat histogram in R
R
ggplot2
hist
updated 23 days ago by
ATpoint
85k • written 23 days ago by
G.S
▴ 60
1
vote
0
replies
173
views
Repeated ensembl IDs in microarray DEG analysis
R
annotation
DEGs
microarray
limma
23 days ago by
Pereira G
▴ 10
0
votes
0
replies
209
views
News:
Course - RNA Sequencing Data with R/Bioconductor
R
Bioconductor
RNA-seq
Differential-Expression-Analysis
updated 26 days ago by
Ram
44k • written 27 days ago by
carlopecoraro2
★ 2.6k
1
vote
2
replies
369
views
Dealing with 2 different layers of counts within RNA assay in seurat
R
seurat
updated 27 days ago by
bk11
★ 3.0k • written 27 days ago by
Varun Gupta
★ 1.3k
0
votes
0
replies
192
views
Salmon transcript-level to gene-level quantification
R
Salmon
RNA-Seq
28 days ago by
Mitmischer
• 0
1
vote
1
reply
244
views
SNP Density plot with custom genome using karyoploteR
NGS
SNP
R
updated 28 days ago by
zx8754
12k • written 28 days ago by
adarsh_munna
▴ 50
3
votes
4
replies
480
views
Cannot process a custom VCF file using bcftools
R
bcftools
VCF
updated 29 days ago by
Pierre Lindenbaum
164k • written 4 weeks ago by
Qiong
▴ 10
4
votes
6
replies
484
views
Pheatmap cluster by columns not working
R
pheatmap
29 days ago by
Bine
▴ 70
7
votes
11
replies
759
views
Sankey + dot plot
R
sankey
gene-ontology
GO
updated 4 weeks ago by
dthorbur
★ 2.5k • written 4 weeks ago by
Sofia
• 0
2
votes
4
replies
411
views
When to use integration with scRNASeq
R
SEURAT
scRNA-seq
updated 4 weeks ago by
Bastien Hervé
5.8k • written 4 weeks ago by
Varun Gupta
★ 1.3k
6
votes
10
replies
2.1k
views
7 follow
Using GEOquery
R
geo
ncbi
updated 4 weeks ago by
Ram
44k • written 2.0 years ago by
Aryan
▴ 40
1
vote
1
reply
308
views
Extracting column from one seurat object based on common column and adding to the other object
R
SEURAT
updated 4 weeks ago by
bk11
★ 3.0k • written 4 weeks ago by
Varun Gupta
★ 1.3k
1
vote
0
replies
187
views
News:
Landscape Genomics course in Poland (January 20-24)
R
LocalAdaptation
Sambada
LandscapeGenomics
LFMM
5 weeks ago by
carlopecoraro2
★ 2.6k
0
votes
1
reply
261
views
NeuronChat: identifyCommunicationPatterns_Neuron() error
R
NeuronChat
4 weeks ago by
sooni
▴ 20
1
vote
1
reply
245
views
Interpreting MA plot - DEG
R
DEG
ggplot2
updated 5 weeks ago by
Ram
44k • written 5 weeks ago by
NEWBIE
• 0
3
votes
2
replies
348
views
Understanding how champ.DMP determines the reference group for phenotypes
phenotype
ChAMP
champ.DMP
R
5 weeks ago by
Benjamin
▴ 10
0
votes
6
replies
459
views
Best practice for gene ontology/pathway/geneset enrichment in 10x data
R
Seurat
scRNA
updated 6 weeks ago by
jared.andrews07
★ 18k • written 6 weeks ago by
yura.grabovska
▴ 600
50 results • Page
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Comment: Magnesium ion in a post-docking adjustment
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[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
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Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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What p-value do you mean? When and how did you calculate it?
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What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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