Showing : rnaseq • reset
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65
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Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 9 days ago by 58k • written 9 days ago by • 0
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3
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119
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 18 days ago by 34k • written 28 days ago by • 0
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3
replies
117
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 18 days ago by 34k • written 19 days ago by • 0
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1
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72
views
Job: Computational Biologist at Chinook Therapeutics
RNASeq Bioconductor Genomics
written 23 days ago by • 0
0
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1
reply
87
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 20 days ago by • 0 • written 24 days ago by • 0
0
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1
reply
121
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 22 days ago by 43k • written 23 days ago by • 0
1
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2
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119
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
24 days ago • updated 23 days ago krawczyk.margarita • 0
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2
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152
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log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
25 days ago • updated 23 days ago Claire • 0
0
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4
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390
views
Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 3.6 years ago by • 0
0
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1
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89
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 24 days ago by ▴ 830 • written 26 days ago by • 0
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0
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51
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EventPointer on TCGA RNA-seq
RNASeq EventPointer
27 days ago Marie • 0
4
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4
replies
152
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Raw RNA-seq data: column names are sequences
RNASeq
updated 4 weeks ago by ▴ 830 • written 4 weeks ago by • 0
0
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6
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246
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DESeq2 - understanding intercept and contrasts
DESeq2 RNASeq
7 weeks ago • updated 5 weeks ago sarah-spie • 0
0
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2
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110
views
Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
6 weeks ago • updated 5 weeks ago peter.zhouyu • 0
0
votes
1
reply
64
views
PCA M3C
M3C RNASeq
updated 5 weeks ago by 3.4k • written 5 weeks ago by • 0
0
votes
1
reply
100
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 5 weeks ago by ★ 27k • written 6 weeks ago by • 0
3
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1
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152
views
Compare two samples by Deseqs
DESeq2 RNASeq
updated 6 weeks ago by 3.4k • written 6 weeks ago by ▴ 10
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2
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148
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
6 weeks ago Ming ▴ 350
0
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3
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129
views
identifying trends in RNA-seq data
RNASeq trend
updated 6 weeks ago by ▴ 830 • written 6 weeks ago by ▴ 620
0
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1
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98
views
What is the best approach to analyze RNA-seq data over 3 time points, but with average 60% missing samples in different time points?
RNASeq
updated 6 weeks ago by 58k • written 6 weeks ago by • 0
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87
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
6 weeks ago camp • 0
0
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2
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110
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AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
6 weeks ago karlaarz • 0
0
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14
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497
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
7 weeks ago • updated 6 weeks ago Abhishek • 0
0
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0
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78
views
WGCNA out of memory
wgcna RNASeq
7 weeks ago zli1 • 0
5
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9
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279
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Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 7 weeks ago by 58k • written 7 weeks ago by ▴ 780
2
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6
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242
views
How can I use geom_label_repel with EnhancedVolcano?
ggrepel RNASeq R EnhancedVolcano
8 weeks ago • updated 7 weeks ago Loren ▴ 10
1
vote
3
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165
views
Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq clusterProfiler enrichplot
8 weeks ago jiro.becker • 0
3
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4
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203
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
9 weeks ago • updated 8 weeks ago sbcn ▴ 70
0
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2
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1.4k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 9 weeks ago by • 0 • written 5.1 years ago by ▴ 40
2
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3
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244
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 9 weeks ago by 34k • written 11 weeks ago by • 0
0
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1
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108
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 9 weeks ago by 58k • written 10 weeks ago by • 0
2
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9
replies
557
views
extract fold change of a list of gene from EdgeR?
EdgeR RNAseq Foldchange
updated 10 weeks ago by ▴ 850 • written 11 weeks ago by • 0
1
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3
replies
192
views
subset a list based on table
edgeR RNASeq resfilt
updated 10 weeks ago by ▴ 830 • written 11 weeks ago by • 0
2
votes
1
reply
220
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2 RNASeq
updated 11 weeks ago by 34k • written 11 weeks ago by • 0
2
votes
1
reply
187
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 12 weeks ago by 3.4k • written 12 weeks ago by • 0
2
votes
1
reply
150
views
Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
edgeR RNASeq
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 150
0
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1
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177
views
Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 3 months ago by 34k • written 3 months ago by • 0
1
vote
1
reply
178
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 3 months ago by 34k • written 3 months ago by • 0
0
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8
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383
views
DESeq2: Variable Importance
DESeq2 RNASeq
updated 3 months ago by 34k • written 3 months ago by • 0
2
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3
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176
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 3 months ago by • 0 • written 3 months ago by • 0
0
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1
reply
139
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 3 months ago by ▴ 650 • written 3 months ago by • 0
5
votes
4
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1.0k
views
Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 3 months ago by 43k • written 3.3 years ago by ▴ 90
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0
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75
views
TCSeq input information
time RNAseq TCSeq
3 months ago curiousmind007 • 0
1
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5
replies
1.1k
views
Error in stattest function
R rnaseq Ballgown
updated 3 months ago by • 0 • written 3.6 years ago by • 0
0
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1
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112
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
3 months ago ayy2110 • 0
4
votes
8
replies
424
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
written 3 months ago by • 0
0
votes
2
replies
309
views
Can't install KEGGprofile
KEGG RNASeq
updated 3 months ago by 58k • written 3 months ago by • 0
0
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1
reply
144
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 3 months ago by 34k • written 3 months ago by • 0
0
votes
1
reply
135
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 3 months ago by 58k • written 3 months ago by • 0
0
votes
1
reply
177
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4 months ago by 34k • written 4 months ago by • 0
50 results • Page 1 of 1
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Comment: Warning messages on Apple M1 BigSur by Alexandre • 0
ok thanks, but that means R will run slower right ? Since Rosetta 2 is emulation environment, correct ?
Answer: Bioinformatics Research Associate, University of Adelaide by keong • 0
I aspire to be a bioinformatics expert, maybe this is the best opportunity for me try this vacancy,thanks for this information great off…
Answer: Effect size using likelihood ratio test in DESeq2 by ATpoint ▴ 830
The thing with time-courses is that you do not necessarily have binary patterns of gene expression changes being only up-or downregulated. …
Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Votes
Answer: Warning messages on Apple M1 BigSur
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
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