Showing : RNAseq • reset
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.4 years ago Julieta • 0
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0
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1.5k
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Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
3.4 years ago estafana.t98 • 0
3
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4
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2.7k
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difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
1
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1
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1.3k
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by ▴ 30
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1
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954
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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0
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783
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
3.4 years ago marymshahi2021 • 0
0
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2
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2.5k
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maSigPro: how to extract the genes in the same cluster
rnaseq
updated 3.4 years ago by • 0 • written 9.8 years ago by ▴ 10
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2
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826
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how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
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1
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1.5k
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Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
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8
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3.3k
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Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 3.5 years ago by ▴ 10
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2
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3.0k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 3.5 years ago by ▴ 270 • written 3.6 years ago by • 0
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0
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870
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.5 years ago osieman52 • 0
4
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5
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3.7k
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Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
1
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1
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860
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
1
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5
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3.5k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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6
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2.4k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.5 years ago Weiqian ▴ 10
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0
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640
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Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
3.5 years ago Pang • 0
1
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1
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1.4k
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Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
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2
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1.5k
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IsoformSwitchAnalyzeR package on mouse data
rnaseq IsoformSwitchAnalyzeR
updated 3.5 years ago by ▴ 120 • written 3.5 years ago by • 0
0
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1
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1.5k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.5 years ago Jenny Drnevich ★ 2.0k
5
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6
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2.9k
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Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.5 years ago Yang Shi ▴ 10
1
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5
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1.5k
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DeSeq2 Matched Analysis
RNASeq DESeq2
3.5 years ago Andrea • 0
3
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4
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1.6k
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Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.5 years ago Yang Shi ▴ 10
1
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2
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3.3k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.6 years ago ClaudiaE • 0
1
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0
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978
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Which algorithm would you use for the cell-cell communication analysis of bulk RNA seq datasets?
RNASeq
3.6 years ago curiousmind007 ▴ 10
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4
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3.8k
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Why Negative value from GSVA
GSVA RNASeq edgeR
3.6 years ago Yang Shi ▴ 10
5
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8
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29k
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Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 18 months ago by ▴ 60 • written 3.6 years ago by ▴ 30
2
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2
replies
1.5k
views
Can't load UCSC transcript IDs
RNASeq
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
2
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4
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2.5k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 10 months ago by 43k • written 3.6 years ago by ▴ 10
3
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3
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1.5k
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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1
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1.0k
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lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
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1
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806
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Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
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1
reply
1.2k
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RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
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1
reply
1.2k
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NOIseq Probability column
RNAseq RNASeqData NOISeq
3.7 years ago • updated 3.6 years ago Pratibha ▴ 10
9
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3
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10k
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Limma vs deseq2 results
limma RNASeq R
3.7 years ago k___ ▴ 30
3
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3
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2.6k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 10
3
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9
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3.4k
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 3.1 years ago by • 0 • written 3.7 years ago by ▴ 20
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2
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2.2k
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Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 3.7 years ago by ▴ 10
1
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1
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2.3k
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Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
1
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2
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1.8k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
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11
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4.6k
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RNA-seq: compare two technical replicates
RNASeq
updated 3.7 years ago by 53k • written 3.8 years ago by ▴ 20
0
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2
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1.0k
views
edgeR
rnaseq edgeR
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
0
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3
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6.9k
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Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by • 0
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6
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4.6k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
3.8 years ago Alan • 0
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0
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1.3k
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.8 years ago chiwut.wong • 0
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0
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1.2k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.8 years ago OST • 0
6
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4
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4.5k
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confused with tximport counts abundance using salmon input
RNASeq tximport
3.8 years ago Al90 ▴ 10
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7
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2.2k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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1
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1.2k
views
Rtracklayer
rtracklayer RNASeq gff
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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1
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1.3k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
1,413 results • Page 5 of 29
Recent ...
Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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