Showing : RnaSeq • reset
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4
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1.2k
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How to analyze 10 samples (5 control, 5 treatment) which perform the experiment from different day
DESeq2 RNASeq
4.1 years ago Yosapol • 0
0
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5
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2.5k
views
RNA-seq with patient samples without replicates with multiple timepoints
edgeR RNASeq multi
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
0
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2
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1.4k
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
0
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2
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1.4k
views
How similar or disimilar are two sets of DEG?
DESeq2 RNASeq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
0
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2
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2.0k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
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1
reply
2.4k
views
Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
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3
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1.5k
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
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2
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2.4k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 20 months ago by • 0 • written 4.2 years ago by • 0
0
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1
reply
1.2k
views
Job: Computational Biologist at Chinook Therapeutics
RNASeq Bioconductor Genomics
written 4.2 years ago by • 0
0
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2
replies
2.2k
views
log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
4.2 years ago Claire • 0
0
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4
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1.3k
views
Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 7.7 years ago by • 0
0
votes
2
replies
2.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.1 years ago by • 0 • written 4.2 years ago by • 0
1
vote
2
replies
1.4k
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
4.2 years ago krawczyk.margarita • 0
5
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4
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11k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.6 years ago by • 0 • written 4.2 years ago by ▴ 10
0
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0
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753
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EventPointer on TCGA RNA-seq
RNASeq EventPointer
4.2 years ago Marie • 0
0
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5
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1.7k
views
DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 3.2 years ago by 43k • written 4.2 years ago by • 0
4
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4
replies
1.6k
views
Raw RNA-seq data: column names are sequences
RNASeq
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
0
votes
1
reply
873
views
PCA M3C
M3C RNASeq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
votes
2
replies
1.8k
views
Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
4.3 years ago peter.zhouyu • 0
0
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1
reply
1.7k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 4.3 years ago by ★ 29k • written 4.3 years ago by ▴ 10
3
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1
reply
1.3k
views
Compare two samples by Deseqs
DESeq2 RNASeq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
0
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3
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1.4k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 3.7 years ago by 53k • written 4.3 years ago by ▴ 380
0
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1
reply
900
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 4.3 years ago by 68k • written 4.3 years ago by • 0
0
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0
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1.1k
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
4.3 years ago camp ▴ 10
2
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6
replies
4.3k
views
DESeq2 - understanding intercept and contrasts
DESeq2 RNASeq
4.3 years ago sarah-spie ▴ 20
0
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3
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1.1k
views
identifying trends in RNA-seq data
RNASeq trend
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by ▴ 670
0
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4
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2.0k
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 2.8 years ago by 68k • written 4.3 years ago by • 0
0
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0
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915
views
WGCNA out of memory
wgcna RNASeq
4.3 years ago zli1 • 0
0
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14
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3.7k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
4.3 years ago Abhishek • 0
5
votes
9
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2.3k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 840
2
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6
replies
6.0k
views
How can I use geom_label_repel with EnhancedVolcano?
ggrepel RNASeq R EnhancedVolcano
4.3 years ago Loren ▴ 10
1
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4
replies
7.2k
views
Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq clusterProfiler enrichplot
updated 3.6 years ago by • 0 • written 4.3 years ago by • 0
3
votes
4
replies
1.9k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
4.3 years ago sbcn ▴ 80
0
votes
1
reply
1.1k
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
1
vote
3
replies
1.2k
views
subset a list based on table
edgeR RNASeq resfilt
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
2
votes
9
replies
3.4k
views
extract fold change of a list of gene from EdgeR?
EdgeR RNAseq Foldchange
updated 4.4 years ago by ★ 1.4k • written 4.4 years ago by • 0
2
votes
1
reply
989
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2 RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
2
votes
1
reply
9.1k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
2
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1
reply
1.4k
views
Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
edgeR RNASeq
updated 4.4 years ago by 53k • written 4.4 years ago by ▴ 780
0
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1
reply
754
views
Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
1
vote
1
reply
1.4k
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
8
replies
2.9k
views
DESeq2: Variable Importance
DESeq2 RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
2
votes
4
replies
1.7k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2.2 years ago by 43k • written 4.4 years ago by • 0
0
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1
reply
1.0k
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 4.5 years ago by ▴ 760 • written 4.5 years ago by • 0
0
votes
0
replies
869
views
TCSeq input information
time RNAseq TCSeq
4.5 years ago curiousmind007 ▴ 10
1
vote
5
replies
3.2k
views
Error in stattest function
R rnaseq Ballgown
updated 4.5 years ago by • 0 • written 7.8 years ago by • 0
0
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1
reply
1.7k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
4.5 years ago ayy2110 • 0
0
votes
2
replies
2.9k
views
Can't install KEGGprofile
KEGG RNASeq
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
votes
2
replies
2.0k
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 3.4 years ago by ▴ 10 • written 4.5 years ago by • 0
0
votes
1
reply
1.1k
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
1,409 results • Page 7 of 29
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Replies
Answer: Alternative to BrainArray custom CDF packages for Affymetrix chips? by Guido Hooiveld ★ 4.1k
It seems that through the Internet Archive these files can be obtained: https://web.archive.org/web/20240710102334/http://brainarray.mbn…
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Votes
Comment: Error installing Seqinfo
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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