0
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2
replies
1.3k
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 23 months ago by 53k • written 23 months ago by • 0
1
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7
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1.9k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 15 months ago by • 0 • written 23 months ago by • 0
0
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0
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673
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Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
23 months ago thomas.heigl.ibk • 0
0
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1
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2.0k
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error in mapIds function
mapIds biomaRt
updated 23 months ago by 700 • written 23 months ago by • 0
1
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3
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1.7k
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DEseq2 coefficient
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23 months ago • updated 21 months ago JKim • 0
3
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5
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1.9k
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DESEQ Inquiry
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updated 23 months ago by 43k • written 23 months ago by ▴ 10
2
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1
reply
810
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 23 months ago by 43k • written 23 months ago by ▴ 10
0
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1
reply
837
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
2
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2
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887
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locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
23 months ago Hope ▴ 10
0
votes
6
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2.8k
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StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 23 months ago by • 0 • written 23 months ago by • 0
0
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2
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921
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problem in installing the new version of bioconductor
ANCOMBC
updated 24 months ago by 4.3k • written 24 months ago by • 0
1
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2
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924
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evaluate the variable importance on genes
DESeq2 deseq
24 months ago Meme • 0
0
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3
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905
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library sizes differ extremely after dds
DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
1
vote
1
reply
810
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Filter genes that have >= 1 cpm and are expressed in 80% of the case in the group (case=Yes, control=No)
RBioinf
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
1
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4
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1.6k
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Comparing gene expression across three tissue types to identify any difference.
DESeq2
24 months ago James Aiden • 0
3
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8
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2.8k
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Downloading package mixOmics
mixOmics
24 months ago noortje_bloem94 • 0
1
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2
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1.1k
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Bioconductor unreachable?
limma
24 months ago edoardo • 0
0
votes
13
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2.0k
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Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 23 months ago by 43k • written 24 months ago by • 0
1
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1
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1.8k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 24 months ago by 68k • written 24 months ago by • 0
3
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1
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1.8k
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Mapping LOC genes between species using Orthology.eg.db (or a similar tool)
Orthology.eg.db
updated 24 months ago by 68k • written 24 months ago by ▴ 30
0
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0
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843
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Job: Statistics Lectureships at St Andrews
JobPosting computational statistics
24 months ago Andy Lynch ▴ 120
7
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3
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1.7k
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work shops/summer schools
written 21.9 years ago by ▴ 50
0
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9
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2.4k
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limma fo continous variables
limma DEGseq
updated 23 months ago by 68k • written 24 months ago by • 0
0
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0
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599
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Comparing the effects of a condition over time in two seperate tissues
MAST
24 months ago Dillon • 0
1
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5
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1.1k
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vst transformation and zero counts
DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by ▴ 740
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4
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2.5k
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Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 24 months ago by 4.3k • written 24 months ago by • 0
1
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12
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3.0k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
24 months ago • updated 23 months ago paria.alipour • 0
0
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3
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877
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problems updating package
TrajectoryGeometry
24 months ago michael.shapiro • 0
0
votes
3
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1.7k
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utf-8 codec can't decode byte 0xd5
importr DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
0
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4
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Seeking Strategies for Managing Duplicate CpG Entries in EPIC v2 Manifest
DNAMethylation EPICv2 IlluminaHumanMethylationEPICmanifest
updated 24 months ago by 68k • written 24 months ago by ▴ 20
0
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2
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893
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limma model matrix questions
limmaGUI limma pairedsamples
24 months ago whyw6948 • 0
0
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1
reply
523
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Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
3
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7
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2.1k
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Average biological replicates in RNA-seq
Mfuzz RNASeq
24 months ago • updated 5 months ago boczniak767 ▴ 740
0
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1
reply
1.7k
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Invalid UTF-8
GeoMxWorkflows
updated 24 months ago by 6.7k • written 24 months ago by • 0
0
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0
replies
787
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how to solve this error?
ChAMPdata ChAMP
24 months ago Meghana • 0
0
votes
3
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1.3k
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DESeq2: Adjust for treatment effect patient vs control
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updated 24 months ago by 43k • written 24 months ago by • 0
0
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1
reply
2.3k
views
Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
0
votes
7
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1.4k
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DESeq filtering specific to contrasts
DESeq2
updated 22 months ago by 43k • written 24 months ago by • 0
0
votes
2
replies
902
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help checking the design matrix and contrast in DESeq2 "not full rank" scenario
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24 months ago • updated 23 months ago ccshao ▴ 70
0
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1
reply
704
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Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
1
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3
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frma normalization
frmaTools affy
updated 24 months ago by 68k • written 24 months ago by • 0
1
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1
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1.1k
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FCS3.2 reading
flowWorkspace flowCore CytoML
updated 22 months ago by ▴ 360 • written 24 months ago by ▴ 30
0
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2
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1.3k
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Limma with replicates at different time points
RNAs limma Differen
24 months ago • updated 23 months ago alessandro • 0
0
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1
reply
762
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Main effect on multiple comparisons in limma
limmaGUI lim MultipleComparison multip
updated 24 months ago by 53k • written 24 months ago by • 0
2
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6
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
24 months ago tsl0026 • 0
5
votes
4
replies
1.2k
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Confusion about LFC using contrasts weights in EdgeR
edgeR
24 months ago pl23 • 0
6
votes
12
replies
6.3k
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Packages don't update, but no error or warning is thrown
Bioconductor
updated 13 months ago by • 0 • written 2.0 years ago by • 0
1
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2
replies
1.0k
views
DESeq2 issue: can't create DESeq2 object
DESeq2 RBioinf
24 months ago Magdalena • 0
0
votes
0
replies
718
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
24 months ago mat149 ▴ 80
2
votes
2
replies
823
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Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 24 months ago by ★ 4.1k • written 24 months ago by • 0
46,748 results • Page 32 of 935
Recent ...
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Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
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Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
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