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questions
0
votes
2
replies
990
views
analysing bismark.cov.gz files
R
methylation
bismark
11 months ago by
adR
▴ 120
1
vote
1
reply
590
views
DESeq2. Multi-factor Interactions designs
RNA-Seq
mikelove
DESeq2
updated 19 months ago by
Marco Pannone
▴ 790 • written 19 months ago by
adR
▴ 120
0
votes
2
replies
652
views
node rewiring analysis using DyNet app in the Cytoscape
Cytoscape
DyNet
20 months ago by
adR
▴ 120
0
votes
0
replies
308
views
Detecting Rewiring Events in Protein-Protein Interaction
interaction
DyNet
network
biology
protein
20 months ago by
adR
▴ 120
0
votes
2
replies
529
views
Is ATAC-seq libraries consider as reduced representation libraries ?
ATAC-Seq
Bismark
2.1 years ago by
adR
▴ 120
0
votes
2
replies
603
views
how to handle duplicate reads in unpaired Whole Exome Sequence
SAMtools
PCR
Picard
updated 11 months ago by
Ram
43k • written 2.1 years ago by
adR
▴ 120
6
votes
11
replies
1.7k
views
how to get legends labels for multiqc plots
multiQC
2.1 years ago by
adR
▴ 120
1
vote
4
replies
674
views
whole exome sequence fragment size analysis
deepTools
bamPEFragmentSize
2.2 years ago by
adR
▴ 120
2
votes
4
replies
945
views
human genome files
alignment
featureCounts
updated 2.2 years ago by
GenoMax
142k • written 2.2 years ago by
adR
▴ 120
0
votes
1
reply
470
views
pipeline for methylation data analysis
ATAC-seq
methyl-ATAC-seq
methylation
DNA
updated 2.2 years ago by
fusion.slope
▴ 250 • written 2.2 years ago by
adR
▴ 120
0
votes
0
replies
320
views
how to add more filter option on the gene ontology(GO) annotation
class
gene
ontology
GO
annotation
2.2 years ago by
adR
▴ 120
2
votes
3
replies
1.8k
views
computeMatrix in deeptool is Running with no result
deepTools
bamCoverage
computeMatrix
updated 2.4 years ago by
sebastian.gregoricchio
▴ 30 • written 2.4 years ago by
adR
▴ 120
2
votes
2
replies
853
views
multiBamSummary for unpaired end read?
multiBamSummary
bamCoverage
deepTools
updated 2.4 years ago by
GenoMax
142k • written 2.4 years ago by
adR
▴ 120
3
votes
6
replies
4.4k
views
multiqc could not generate results
multiQC
updated 2.4 years ago by
Phil Ewels
★ 1.4k • written 2.4 years ago by
adR
▴ 120
2
votes
3
replies
839
views
how to do basic statistics for bam files
picard
GATK
alignment
updated 2.5 years ago by
colindaven
6.4k • written 2.5 years ago by
adR
▴ 120
1
vote
5
replies
6.9k
views
how to install picard and GATK
picard
GATK
updated 2.5 years ago by
Pierre Lindenbaum
161k • written 2.5 years ago by
adR
▴ 120
1
vote
1
reply
799
views
feutureCount in the subread
fe
subread
2.5 years ago by
adR
▴ 120
1
vote
6
replies
1.2k
views
counting EXOM reads using subread featureCounts
featureCounts
subread
exom
updated 23 months ago by
Ram
43k • written 2.5 years ago by
adR
▴ 120
2
votes
3
replies
922
views
alignment using bowtie2
bowtie2
sequencing
alignment
updated 2.5 years ago by
Carlo Yague
8.7k • written 2.5 years ago by
adR
▴ 120
1
vote
3
replies
940
views
Differentail expression analysis between 3 groups
RNA-Seq
DESeq2
limma
DEA
updated 2.5 years ago by
Basti
★ 2.0k • written 2.5 years ago by
adR
▴ 120
0
votes
0
replies
353
views
Circulating Cell-Free DNA
Bioconductor
R
sequencing
2.6 years ago by
adR
▴ 120
0
votes
2
replies
752
views
how to produce plot below using R
RNA-Seq
plot
circus
2.8 years ago by
adR
▴ 120
0
votes
1
reply
451
views
gene calssfication based on on their chemical nature
RNA-Seq
SingleCellSignalR
updated 2.9 years ago by
Nitin Narwade
★ 1.6k • written 2.9 years ago by
adR
▴ 120
0
votes
0
replies
432
views
circusplot:-adding additional layer or track to indicate additional futures
r
2.9 years ago by
adR
▴ 120
0
votes
1
reply
593
views
Inter-tissue coexpression network analysis
correlation
bipartite
clustring
coexpression
3.2 years ago by
adR
▴ 120
2
votes
4
replies
3.3k
views
how to make correlation heatmap
heatmaps
correlation
updated 3.2 years ago by
Eugene A
▴ 180 • written 3.2 years ago by
adR
▴ 120
0
votes
0
replies
544
views
possiblity of using SingleCellSignalR for bulk RNAseq data
RNA-Seq
SingleCellSignalR
3.2 years ago by
adR
▴ 120
0
votes
5
replies
1.2k
views
MEgene correlated to triat and Gene signficance coorelated to triat
WGCNA
andres.firrincieli
updated 3.1 years ago by
eggerj
▴ 40 • written 3.2 years ago by
adR
▴ 120
0
votes
2
replies
850
views
how to plot a heatmap with out dendogram using function TOMplot() in WGCNA
WGCNA
heatmap
r
3.3 years ago by
adR
▴ 120
9
votes
4
replies
1.1k
views
interprating PCA plot
PCA
RNA-Seq
updated 5 months ago by
ATpoint
82k • written 3.3 years ago by
adR
▴ 120
0
votes
0
replies
884
views
how to plot selected enriched pathways using emapplot
r
Guangchuang Yu
clusterProfiler
updated 3.3 years ago by
Biostar
20 • written 3.3 years ago by
adR
▴ 120
4
votes
6
replies
1.3k
views
genes not mapping to ENTREZID
gene
ENTREZID
pathway
KEGG
written 3.3 years ago by
adR
▴ 120
0
votes
1
reply
731
views
Two-dimensional hierarchically clustered heatmap
heatmap
cluster
corrlation
R
updated 3.4 years ago by
ATpoint
82k • written 3.4 years ago by
adR
▴ 120
1
vote
4
replies
881
views
gene network analysis for 3 conduation
gene network
updated 3.5 years ago by
Kevin Blighe
88k • written 3.5 years ago by
adR
▴ 120
0
votes
10
replies
1.7k
views
correlation matrix and working on signficant genes
co-expression
corrlation
3.5 years ago by
adR
▴ 120
1
vote
3
replies
725
views
How to analyze RNAseq data
r
RNA-Seq
updated 3.5 years ago by
ATpoint
82k • written 3.6 years ago by
adR
▴ 120
0
votes
2
replies
723
views
correlation of genes
RNA-Seq
correlation
updated 3.6 years ago by
JC
13k • written 3.6 years ago by
adR
▴ 120
0
votes
0
replies
611
views
Signal pathway impact analysis
R
pathway
updated 3.6 years ago by
Biostar
20 • written 3.7 years ago by
adR
▴ 120
1
vote
1
reply
926
views
correlation of genes from two data sets
RNA-Seq
correlation
r
3.6 years ago by
adR
▴ 120
0
votes
0
replies
667
views
gene network analysis
network
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 3.6 years ago by
adR
▴ 120
1
vote
3
replies
946
views
How I can study cross-talk from two different tissue using gene expression profile
RNA-Seq
R
3.7 years ago by
adR
▴ 120
0
votes
4
replies
1.1k
views
how to apply volcano plot for genes predicting a phenotype
r
volcanoplot
enchanced volcanoplots
3.7 years ago by
adR
▴ 120
4
votes
4
replies
2.5k
views
volcanoplots with different colors for up/down regulated genes
EnhancedVolcano
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
adR
▴ 120
1
vote
2
replies
3.1k
views
Warning messages: gene set enrichment analysis with clusterProfiler
r
clusterProfiler
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
adR
▴ 120
0
votes
6
replies
1.1k
views
predicting some phenotype by gene
RNA-Seq
limm
updated 3.8 years ago by
Biostar
20 • written 3.8 years ago by
adR
▴ 120
1
vote
1
reply
776
views
genes popup in the volcano plots
enchancedvolca
3.8 years ago by
adR
▴ 120
4
votes
1
reply
1.7k
views
enrichment analysis using cluster profiler
clusterProfiler
R
Biocondactor
updated 3.8 years ago by
Papyrus
★ 2.9k • written 3.8 years ago by
adR
▴ 120
1
vote
4
replies
976
views
How to download matrix of the "GSE73554"
RNA-Seq
updated 14 months ago by
Ram
43k • written 3.9 years ago by
adR
▴ 120
0
votes
0
replies
740
views
difference between bitr function and mapIds function
gene ontology
3.9 years ago by
adR
▴ 120
2
votes
1
reply
1.4k
views
Gene Ontology using clusterProfiler
RNA-Seq
3.9 years ago by
adR
▴ 120
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