Showing : Visualization • reset
4
votes
2
replies
722
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
0
votes
2
replies
989
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
0
replies
557
views
Catalyst::cluster function does NOT produce the same results when setting seed
visua Visualization CATALYST
17 months ago elefth.pavlos ▴ 40
5
votes
11
replies
6.8k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 24 months ago by ▴ 20
0
votes
2
replies
1.3k
views
ggplot2 bar plot
R Visualization ggplot2
2.6 years ago Jitendra ▴ 10
4
votes
6
replies
2.0k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
3.0 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.3k
views
Unable to label in Enhanced Volcano
Visualization
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
0
votes
4
replies
2.0k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
1
vote
1
reply
1.5k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
4.2 years ago Luo Weijun ★ 1.6k
1
vote
3
replies
2.4k
views
copy number variation analysis (CNV)
copynumber plot visualization NGS gene
updated 4.4 years ago by ▴ 220 • written 4.6 years ago by • 0
2
votes
2
replies
1.6k
views
Can't display protein domain data from UCSC table unipDomain using Gviz
Gviz protein visualization UcscTrack protein domains
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 10
5
votes
11
replies
2.1k
views
Visualization tool for GC-bias in SE data?
GC-bias ALPINE visualization
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 20
0
votes
0
replies
977
views
Sample grouping (phenoData) and visualization in R package- HtqPCR
HtqPCR grouping visualization R phenoData
5.8 years ago mohammedtoufiq91 ▴ 10
0
votes
9
replies
2.5k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
9
replies
16k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.3 years ago by • 0
2
votes
2
replies
1.4k
views
What can be done to separate the healthy and patient samples in PCA plot and Distance matrix
deseq2 PCAplot Visualization
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
vote
2
replies
1.7k
views
Package for custom visualization of multiple sequence alignment
MSA visualization
updated 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
3
votes
3
replies
1.3k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Netbiov vertex.color vector length error
netowrk visualization
6.8 years ago Wojeff • 0
0
votes
4
replies
1.8k
views
Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
8
votes
12
replies
12k
views
EdgeR: Explaning dispersion types to newbies
edger dispersion estimatedispersions visualization teaching
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 20
0
votes
0
replies
1.5k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
7.3 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.3k
views
spotSegmentation package: How to "display the entire block of segmented spots at the end of processing"
spotsegmentation argument visualization
7.7 years ago rene_houtman • 0
2
votes
4
replies
2.0k
views
chimeraviz - import own fusion file for visualization
visualization chimeraviz
updated 3.8 years ago by • 0 • written 7.9 years ago by ▴ 10
0
votes
0
replies
1.8k
views
News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
8.0 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.5k
views
Change DEXSeq plot: Intron length/width and genes from - strand
rnaseq r dexseq visualization
8.0 years ago aleipz • 0
0
votes
3
replies
2.6k
views
RNAseq read coverage plot: What tool?
rnaseq visualization plotcoveragehist
updated 8.1 years ago by ★ 1.3k • written 8.1 years ago by ▴ 130
2
votes
2
replies
5.6k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2 clusterprofiler visualization gseGo
8.1 years ago • updated 4.5 years ago tcalvo ▴ 100
0
votes
2
replies
1.8k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 8.3 years ago by ▴ 230 • written 8.3 years ago by • 0
0
votes
7
replies
2.7k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 8.7 years ago by • 0 • written 15.1 years ago by ★ 1.6k
1
vote
0
replies
1.8k
views
News: BioCAsia, 4th November 2016, Brisbane, Australia
conference transcription epigenomics visualization infrastructure News
8.9 years ago Matthew Ritchie ▴ 1000
0
votes
1
reply
1.5k
views
Survey on interactive visualization and Bioconductor
visualization epivizr
9.0 years ago • updated 8.9 years ago Hector Corrada Bravo ▴ 60
0
votes
1
reply
1.7k
views
ChIPseeker gene body plot
chipseeker visualization
updated 9.0 years ago by ★ 1.2k • written 9.0 years ago by ▴ 50
7
votes
0
replies
4.2k
views
Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
9.2 years ago Vincent J. Carey, Jr. 6.7k
0
votes
0
replies
1.9k
views
Pathview Web Server: user friendly pathway visualization and data integration
pathview pathway analysis visualization web server omics data
9.4 years ago Weijun Luo • 0
3
votes
5
replies
2.8k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 9.5 years ago by ★ 1.6k • written 9.5 years ago by ▴ 840
0
votes
5
replies
3.3k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by • 0
3
votes
0
replies
2.0k
views
News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
9.9 years ago • updated 9.8 years ago Matthew Ritchie ▴ 1000
0
votes
0
replies
1.8k
views
flowWorkspace and ggcyto
flowworkspace flow cytometry visualization
9.8 years ago Jiang, Mike ★ 1.3k
11
votes
0
replies
6.3k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
9.9 years ago Martin Morgan 25k
8
votes
0
replies
4.0k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.9 years ago Martin Morgan 25k
1
vote
3
replies
2.4k
views
Visualizing gene counts and variance stabilization
deseq2 rnaseq variancestabilizingtransformation visualization
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 40
0
votes
2
replies
4.3k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 9.9 years ago by ★ 1.6k • written 9.9 years ago by ▴ 130
0
votes
1
reply
1.8k
views
Graphic representation of mroast results
mroast visualization
10.0 years ago Elena Serrano ▴ 30
1
vote
2
replies
3.3k
views
gene expression visualization: lineplot with ggplot2
ggplot2 lineplot visualization
updated 10.0 years ago by ▴ 180 • written 10.0 years ago by ▴ 130
0
votes
0
replies
1.7k
views
Circos Styling plots is now easy with canceR package
canceR visualization omiccircos
10.0 years ago kmezhoud ▴ 10
1
vote
1
reply
1.7k
views
Visualizing Structural variants
visualization SV
updated 10.1 years ago by 6.7k • written 10.1 years ago by ▴ 190
0
votes
0
replies
2.0k
views
Job: Post-Doctoral Research Fellow - Patient Genomics Data Visualization
visualization genomics personalized medicine systemsbiology js Job
10.1 years ago Hamid Bolouri ▴ 50
0
votes
7
replies
5.6k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
10.1 years ago svlachavas ▴ 840
1
vote
0
replies
2.2k
views
Job: PhD position - Heidelberg: Bioinformatic analysis of high-throughput and image-based RNAi screening data
high-throughput screening RNAi image analysis data integration visualization Job
10.2 years ago e.schmidt ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Limma suqeezeVar by Gordon Smyth 52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
Comment: Discrepancies in normalised count data vs unnormalised by swbarnes2 ★ 1.4k
Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…
Comment: Can't install BioC packages (and manager) behind firewall by Marcel Ramos 700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa by Alejandro • 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error by asafpr • 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Votes
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
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