0
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2
replies
878
views
Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
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written 17 months ago by • 0
1
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2
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528
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Deseq2 - differenc in results
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3
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3
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voom does not seem to properly correct for library size
limma
updated 17 months ago by 53k • written 17 months ago by ★ 5.0k
1
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3
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651
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Missing test data for RiboProfiling package
RiboProfiling
updated 17 months ago by 68k • written 17 months ago by • 0
2
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8
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1.5k
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AffylmGUI does not start wit R 4.4.1
affylmGUI
updated 16 months ago by 53k • written 17 months ago by ▴ 30
0
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7
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1.2k
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DESeq design with and without intercept is giving different results
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written 17 months ago by • 0
1
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5
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1.7k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 17 months ago by 53k • written 17 months ago by • 0
1
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3
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1.7k
views
Non-zero exit status error when installing GenomeInfoDbData
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written 17 months ago by • 0
0
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3
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1.0k
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Merging multi-fastq samples in recount3
recount3
written 17 months ago by • 0
0
votes
2
replies
1.4k
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recount
recount
updated 17 months ago by ★ 1.1k • written 3.7 years ago by • 0
0
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3
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1.2k
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 17 months ago by • 0
0
votes
0
replies
765
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Job: PhD position: Analysis of epistatic interactions in enzymes using long-read sequencing data
NGS AI Bioconductor
updated 17 months ago by ▴ 10 • written 17 months ago by ▴ 180
0
votes
0
replies
575
views
BioCAsia 2024 Abstract Deadline - August 26th
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17 months ago Maria Doyle ▴ 110
0
votes
3
replies
1.0k
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 17 months ago by 53k • written 17 months ago by • 0
0
votes
1
reply
496
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CleanUpRNAseq package
CleanUpRNAseq
updated 17 months ago by ▴ 20 • written 17 months ago by • 0
0
votes
3
replies
819
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Create TidySummarizedExperiment from RangedSummarizedExperiment?
tidyomics
written 17 months ago by • 0
0
votes
3
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1.5k
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flowAI: flow rare check in R vs FlowJo
flowAI
updated 17 months ago by • 0 • written 23 months ago by • 0
0
votes
2
replies
732
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Analysis of transcription inhibition with DESeq2
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written 17 months ago by • 0
2
votes
4
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1.7k
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# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 17 months ago by 68k • written 17 months ago by • 0
6
votes
5
replies
4.7k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 12 months ago by ▴ 20 • written 17 months ago by • 0
0
votes
1
reply
773
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
17 months ago • updated 11 months ago Ian D. ▴ 70
0
votes
1
reply
1.0k
views
installing "org.Hs.eg.db",go error
org.Hs.eg.db
updated 17 months ago by 4.3k • written 17 months ago by • 0
4
votes
5
replies
13k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 17 months ago by • 0 • written 8.3 years ago by ▴ 60
3
votes
4
replies
1.4k
views
using limma trend workflow in CAMERA
CAMERA limma
17 months ago Jiahao Tian • 0
0
votes
0
replies
531
views
Are equal whisker lengths important in an RLE plot?
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17 months ago BioinfGuru ▴ 70
0
votes
0
replies
775
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News: EuroBioC Updates: Important Deadlines
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17 months ago Maria Doyle ▴ 110
3
votes
3
replies
1.8k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
2
replies
1.3k
views
R is Removing the Gene Names in My Count Data
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updated 17 months ago by ▴ 70 • written 17 months ago by • 0
1
vote
4
replies
1.6k
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
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17 months ago Bob ▴ 30
0
votes
1
reply
655
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
2
replies
1.1k
views
DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 17 months ago by • 0 • written 17 months ago by • 0
3
votes
3
replies
1.1k
views
One-sided tests with CAMERA-PR
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updated 17 months ago by 53k • written 17 months ago by ▴ 10
0
votes
2
replies
1.0k
views
FlowSOM library requires igraph but igraph does not install
FlowSOM
updated 9 months ago by • 0 • written 17 months ago by • 0
0
votes
2
replies
547
views
get_snp
frmaTools
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
0
replies
616
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
17 months ago user_bioinfo • 0
0
votes
3
replies
1.2k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
3
votes
5
replies
2.6k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
2
votes
1
reply
1.8k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
0
votes
1
reply
672
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
17 months ago mdidish ▴ 10
0
votes
0
replies
563
views
DiffBind dba.plotprofile y-axis range
DiffBind
17 months ago Tara • 0
2
votes
4
replies
892
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Bioconductor Submission question
Bioconductor
17 months ago XFWu • 0
2
votes
3
replies
1.4k
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
17 months ago BioinfGuru ▴ 70
2
votes
2
replies
945
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
17 months ago BioinfGuru ▴ 70
0
votes
0
replies
498
views
proActiv-promoter analysis
proActiv Transcriptomics
17 months ago wang.xiangyu • 0
2
votes
1
reply
2.6k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 17 months ago by ★ 29k • written 17 months ago by • 0
0
votes
0
replies
593
views
News: Annual Nominations Open for CAB and TAB! Deadline Aug 31
TAB CAB Bioconductor
17 months ago shepherl 4.3k
1
vote
2
replies
837
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
17 months ago DL • 0
0
votes
3
replies
759
views
How to combine multiple lists of cytoframes/cytocq data objects into one
flowWorkspace cytocq
updated 17 months ago by ▴ 360 • written 17 months ago by ▴ 30
0
votes
1
reply
875
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 17 months ago by 53k • written 17 months ago by • 0
1
vote
4
replies
1.6k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
17 months ago kschecht • 0
1,000 results • Page 18 of 20
Recent ...
Replies
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. Your use…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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