Showing : visualization • reset
4
votes
2
replies
665
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 months ago by ★ 4.8k • written 4 months ago by ▴ 10
0
votes
2
replies
955
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
0
replies
551
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
6.6k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 23 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 • updated 2.9 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.3k
views
Unable to label in Enhanced Volcano
Visualization
updated 3.3 years ago by ★ 4.0k • written 3.3 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 • updated 4.1 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 4.5 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 4.6 years ago by 68k • written 4.6 years ago by ▴ 10
5
votes
11
replies
2.0k
views
Visualization tool for GC-bias in SE data?
GC-bias ALPINE visualization
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 20
0
votes
0
replies
972
views
Sample grouping (phenoData) and visualization in R package- HtqPCR
HtqPCR grouping visualization R phenoData
5.7 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 6.2 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 6.5 years ago by ▴ 20 • written 6.5 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
7.2 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
7.6 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 7.8 years ago by ▴ 10
0
votes
0
replies
1.7k
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 8.0 years ago by ★ 1.3k • written 8.0 years ago by ▴ 130
2
votes
2
replies
5.5k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2 clusterprofiler visualization gseGo
8.0 years ago • updated 4.4 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 15.0 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
8.8 years ago Matthew Ritchie ▴ 1000
0
votes
1
reply
1.5k
views
Survey on interactive visualization and Bioconductor
visualization epivizr
8.9 years ago Hector Corrada Bravo ▴ 60
0
votes
1
reply
1.7k
views
ChIPseeker gene body plot
chipseeker visualization
updated 8.9 years ago by ★ 1.2k • written 8.9 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
9.1 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
9.3 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 9.5 years ago by ★ 1.6k • written 9.5 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 9.7 years ago Matthew Ritchie ▴ 1000
0
votes
0
replies
1.7k
views
flowWorkspace and ggcyto
flowworkspace flow cytometry visualization
9.7 years ago Jiang, Mike ★ 1.3k
11
votes
0
replies
6.2k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
9.8 years ago Martin Morgan 25k
8
votes
0
replies
3.9k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.8 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
4.2k
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
9.9 years ago Elena Serrano ▴ 30
1
vote
2
replies
3.3k
views
gene expression visualization: lineplot with ggplot2
ggplot2 lineplot visualization
updated 9.9 years ago by ▴ 180 • written 9.9 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 10.0 years ago by 6.7k • written 10.0 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
5.5k
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
10.1 years ago e.schmidt ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
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