0
votes
2
replies
1.0k
views
DESeq2 design matrix choice
deseq2 design matrix
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
6
replies
3.5k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
0
votes
1
reply
1.9k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 2.7 years ago by • 0 • written 6.4 years ago by • 0
0
votes
1
reply
1.2k
views
Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap?
DiffBind plot plotHeatmap dba.plotHeatmap
updated 6.4 years ago by ★ 5.2k • written 6.5 years ago by • 0
0
votes
2
replies
1.6k
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot rna seq
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
vote
3
replies
1.7k
views
BSgenomeForge version 1.52.0, error in .TwoBits_export
bsgenome forge twobits_export bioconductor
6.4 years ago bioinagesh • 0
5
votes
5
replies
2.9k
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 5.0 years ago by ★ 1.6k • written 6.4 years ago by ▴ 10
1
vote
1
reply
1.4k
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
0
votes
1
reply
986
views
error installing RforMassSpectrometry
RforMassSpectrometry ProtGenerics
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
3
votes
2
replies
1.6k
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DESeq2 for big data sets
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
1
reply
1.3k
views
Bio Conductor offline installation
software error
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
2
votes
7
replies
3.2k
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RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
2
votes
2
replies
1.3k
views
Statistics for within-condition transcript abundance comparisons
rnaseqDTU
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
votes
1
reply
1.5k
views
edgeR default normalization method
edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
2
votes
3
replies
9.2k
views
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager
software error
6.5 years ago • updated 6.4 years ago Aki Hoji ▴ 10
1
vote
6
replies
3.1k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
6.5 years ago • updated 6.4 years ago sabrina.mcnew • 0
0
votes
0
replies
391
views
System Crash with Command "removeBimeraDenovo"
software error
6.5 years ago himani.khurana1 • 0
0
votes
2
replies
2.0k
views
DESeq2 installs but then can't be brought in as a library
deseq2 R3.6.1 library(DESeq2)
updated 3.3 years ago by • 0 • written 6.5 years ago by • 0
2
votes
2
replies
1.7k
views
DESeq2 error due to zeros
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 20
1
vote
4
replies
2.4k
views
MBDseq analysis using qsea package
qsea MBDseq
updated 13 months ago by ▴ 20 • written 6.5 years ago by • 0
0
votes
1
reply
1.8k
views
Rsamtools: how to extract uniquely aligned single-end or paired-end by ScanbamParam
Rsamtools
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 90
0
votes
2
replies
1.8k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
6
replies
2.9k
views
why org.Hs.egGO2ALLEGS contain genes number difference from GO database?
org.Hs.eg.db org.Hs.egGO2ALLEGS
updated 3.6 years ago by • 0 • written 6.5 years ago by • 0
0
votes
1
reply
1.3k
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 20 months ago by • 0 • written 6.5 years ago by ▴ 80
2
votes
1
reply
3.1k
views
DESeq2 heatmap and rlog transformed values
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
1
vote
3
replies
2.2k
views
ggbio - change transcript label sizes
ggbio annotation
updated 3.8 years ago by ▴ 50 • written 6.5 years ago by ★ 4.0k
1
vote
3
replies
2.8k
views
Correct way to split and unsplit a DataFrame
s4vectors iranges
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 90
0
votes
5
replies
1.0k
views
Phyloseq to DESeq2 Help
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
2
replies
1.5k
views
Can we control colors for two different colAtributes
diffbind plot plotHeatmap
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
5
votes
7
replies
12k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
2
votes
1
reply
5.1k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
6.5 years ago endrebak85 ▴ 40
0
votes
0
replies
1.5k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
6.5 years ago tatabox • 0
0
votes
2
replies
1.3k
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NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
1
reply
1.9k
views
DiffBind dba error
DiffBind dba R error
updated 6.5 years ago by ★ 5.2k • written 6.7 years ago by • 0
0
votes
2
replies
1.7k
views
DiffBind dba.count error pv$merge(bed): attempt to apply non-function
DiffBind
updated 6.5 years ago by ★ 5.2k • written 6.7 years ago by • 0
0
votes
4
replies
1.8k
views
diffbind dba.plotvolcano bLabels option use genames instead of numbers
diffbind
updated 6.5 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
0
votes
2
replies
856
views
How can we increase the width of the correlation plot generated by DiffBind
DiffBind plot(DBdata)
updated 6.5 years ago by ★ 5.2k • written 6.6 years ago by • 0
2
votes
2
replies
1.4k
views
DESeq2 s-value threshold for FSOS events
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
3
replies
2.3k
views
diffbind dba object subset peak regions
diffbind
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by ▴ 160
0
votes
1
reply
1.1k
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
0
votes
5
replies
4.8k
views
How can I remove the row and column labels/names in the plot() or dba.plotHeatmap() while plotting correlation matrix using diffbind?
Diffbind plot heatmap.3
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
1
vote
1
reply
1.7k
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
6.5 years ago konstantinos.bogias ▴ 10
0
votes
1
reply
860
views
DESeq2 Wald test p-values
deseq2
6.5 years ago Homer • 0
0
votes
1
reply
2.5k
views
package DESeqDataSet is not available for R version 3.6.1
deseq2
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
2
replies
830
views
DESeq2: Paired multifactor test with batch effect - one or more variables in design formula are linear combinations of others
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 60
0
votes
9
replies
2.1k
views
GVIZ stacking error
gviz
6.5 years ago d.depledge • 0
0
votes
2
replies
840
views
DESeq2 rlog as the input for ARACNE
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
2
votes
4
replies
1.7k
views
Are there any functions to subtract all features(rows) to a particular value(row) in the same data file?
R python normalization matrix
updated 6.5 years ago by ▴ 30 • written 6.5 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Job: Bioinformatics Analyst II, Genomics Shared Resource (Seattle, WA)
GENOMICS BIOINFORMATICS SEATTLE R PYTHON Job
6.5 years ago Fred Hutch (Recruiting) ▴ 40
0
votes
8
replies
4.7k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 6.5 years ago by • 0 • written 8.1 years ago by ▴ 20
46,743 results • Page 199 of 935
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Comment: Chip Seq Analysis of RNA Polymerase 2 by Tikaaaq2c • 0
Without proper scaling or an enrichment check , Pol 2 peaks can appear flat against the background. If the data remains noisy, you might w…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by Tikaaaq2c • 0
Organizing complex transcripts requires the same discipline as managing a digital library on a learning platform. Many researchers use a [S…
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
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No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
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In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
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Answer: Limma-voom sample weights and impact on DEG numbers
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