Showing : Network • reset
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
5
votes
14
replies
4.8k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 8.4 years ago by ★ 8.2k • written 8.4 years ago by ▴ 50
0
votes
12
replies
2.2k
views
new package for generating interactive HTML reports
Network limma GOstats GSEAlm edgeR ReportingTools Network limma GOstats GSEAlm edgeR
updated 11.3 years ago by ★ 1.6k • written 11.3 years ago by ▴ 20
0
votes
10
replies
2.4k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
11.1 years ago Julie Zhu ★ 4.3k
1
vote
10
replies
2.0k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 17 months ago by • 0
7
votes
9
replies
3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 15 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
0
votes
8
replies
1.7k
views
Visualization of metabolic network in lpSolve format
Network Network
11.1 years ago Denis Kazakiewicz ▴ 70
0
votes
7
replies
1.5k
views
GeneAnswer package Query
Network graph Network graph
updated 11.6 years ago by ▴ 300 • written 11.7 years ago by ▴ 570
0
votes
7
replies
1.2k
views
(no subject)
Network Network
updated 11.0 years ago by 50k • written 11.0 years ago by ▴ 60
1
vote
7
replies
2.7k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
9.5 years ago pshannon ▴ 100
0
votes
7
replies
1.8k
views
Kegg pathway --> gene network
Pathways Network Pathways Network
updated 15.3 years ago by 25k • written 15.4 years ago by ▴ 40
2
votes
6
replies
4.6k
views
Error running TOMplot in WGCNA package
wgcna network
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
0
votes
6
replies
1.5k
views
Network install of packages
Network Network
updated 15.5 years ago by 21k • written 15.5 years ago by ▴ 20
0
votes
6
replies
1.4k
views
Regarding KEGGgraph
Pathways Network PROcess Pathways Network PROcess
updated 14.3 years ago by ★ 13k • written 14.3 years ago by ▴ 270
0
votes
5
replies
3.5k
views
Adjacency to network using R
Visualization Network convert Visualization Network convert
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ▴ 120
2
votes
5
replies
1.3k
views
runing NetBenchmark on my own datasets
software error network
updated 8.5 years ago by ▴ 20 • written 8.5 years ago by ▴ 40
8
votes
4
replies
6.9k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by ▴ 180
0
votes
4
replies
1.5k
views
Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 13.0 years ago by ▴ 310 • written 13.0 years ago by ★ 8.2k
0
votes
4
replies
1.4k
views
[R] RCytoscape setPosition error
Network Cancer graph Network Cancer graph
updated 13.2 years ago by ▴ 250 • written 13.2 years ago by ★ 1.1k
0
votes
4
replies
1.3k
views
Example of converting graphNEL object to ajacency matrix?
Network convert Network convert
updated 16.0 years ago by ★ 5.5k • written 16.0 years ago by ▴ 50
2
votes
4
replies
1.8k
views
Case-control study using WGCNA
wgcna network rna-seq
4.4 years ago ag1805x ▴ 80
0
votes
3
replies
1.9k
views
Drawing network graphs (i.e. nodes and edges)
Network Network
updated 18.2 years ago by ▴ 360 • written 18.2 years ago by ▴ 170
0
votes
3
replies
1.1k
views
rna-seq
Microarray Pathways Network goseq Microarray Pathways Network goseq
updated 11.6 years ago by ▴ 350 • written 11.6 years ago by ★ 13k
0
votes
3
replies
554
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
9 months ago Alexandros • 0
4
votes
3
replies
902
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.0 years ago by ★ 3.0k • written 5.0 years ago by ▴ 80
0
votes
3
replies
1.3k
views
building enzyme centric metabolic network
Network KEGGSOAP Network KEGGSOAP
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 270
0
votes
3
replies
1.7k
views
identifying network communities in a protein-protein interaction graph
Network Network
updated 14.3 years ago by ▴ 80 • written 14.3 years ago by ▴ 190
0
votes
3
replies
2.3k
views
WGCNA chooseTopHubInEachModule function
Network Network
11.9 years ago Sudeep Sahadevan ▴ 20
0
votes
3
replies
1.4k
views
tool for drawing interaction network
Pathways Network Pathways Network
updated 13.9 years ago by ▴ 220 • written 13.9 years ago by ★ 3.9k
0
votes
2
replies
5.9k
views
WGCNA package
Network Network
updated 10.1 years ago by ★ 3.0k • written 10.1 years ago by ▴ 130
0
votes
2
replies
3.9k
views
Gene filtering for RNA-seq data
Normalization GO Network HTSFilter DESeq2 Normalization GO Network HTSFilter DESeq2
updated 10.4 years ago by 41k • written 10.4 years ago by ★ 13k
4
votes
2
replies
1.1k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
votes
2
replies
1.2k
views
limma for homemade microarray - question on NAs and multiple probes for one gene
Microarray Normalization GO Network Cancer probe limma Microarray Normalization GO probe
updated 10.8 years ago by 50k • written 10.8 years ago by ★ 3.0k
0
votes
2
replies
2.1k
views
Soft-threshold in WGCNA
wgcna network bicor threshold
updated 3.7 years ago by ★ 3.0k • written 3.7 years ago by ▴ 80
0
votes
2
replies
321
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
5
votes
2
replies
4.1k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 30
0
votes
2
replies
1.4k
views
IdeogramTrack and bigWig file errors in Gviz
Network rtracklayer CAMERA Gviz Network rtracklayer CAMERA Gviz
11.0 years ago Michael Lawrence ★ 11k
3
votes
2
replies
5.0k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 23 months ago by ▴ 10 • written 3.7 years ago by ▴ 80
0
votes
2
replies
1.1k
views
Error in gammaFitEM for library(lumi) [Possible Bug]
Preprocessing Network Preprocessing Network
updated 12.2 years ago by ▴ 440 • written 12.2 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Affymetrix MASv5 code & sample data
Network Network
updated 18.9 years ago by ★ 1.8k • written 18.9 years ago by ▴ 50
0
votes
2
replies
1.4k
views
bug in rendering reciprocal edges?
Network graph Rgraphviz Network graph Rgraphviz
updated 12.7 years ago by ▴ 340 • written 12.7 years ago by ▴ 20
0
votes
2
replies
2.7k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
8.3 years ago hywel.williams • 0
1
vote
2
replies
1.3k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 7.9 years ago by ▴ 120 • written 7.9 years ago by ▴ 660
0
votes
2
replies
905
views
KEGG analysis
Network Cancer Network Cancer
15.1 years ago Daniel Brewer ★ 1.9k
0
votes
2
replies
1.5k
views
RV: wgcna
Network Cancer Network Cancer
updated 12.8 years ago by ★ 3.3k • written 12.8 years ago by ▴ 50
0
votes
2
replies
1.0k
views
Network plot
Network Network
updated 13.8 years ago by 21k • written 13.8 years ago by ▴ 100
1
vote
2
replies
2.8k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
8.9 years ago cristina della beffa ▴ 30
0
votes
2
replies
1.4k
views
proposed: a bridge between R and Cytoscape
Visualization Network graph Visualization Network graph
updated 13.8 years ago by ★ 13k • written 13.9 years ago by ★ 1.1k
0
votes
2
replies
1.3k
views
AgiMicroRna package is not available at bioconductor or not in active form???
Microarray Network microRNA AgiMicroRna Microarray Network microRNA AgiMicroRna
updated 14.1 years ago by ▴ 60 • written 14.1 years ago by 21k
1
vote
2
replies
4.0k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
50 results • Page 1 of 1
Recent ...
Replies
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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