Showing : RNASeq • reset
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735
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
3.2 years ago marymshahi2021 • 0
0
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2
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2.4k
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maSigPro: how to extract the genes in the same cluster
rnaseq
updated 3.2 years ago by • 0 • written 9.6 years ago by ▴ 10
1
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2
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787
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how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
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1
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1.4k
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Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
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8
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3.0k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 3.2 years ago by ▴ 10
0
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2
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2.6k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 3.2 years ago by ▴ 270 • written 3.4 years ago by • 0
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0
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819
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.2 years ago osieman52 • 0
4
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5
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3.5k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 3.2 years ago by 43k • written 3.3 years ago by ▴ 10
1
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1
reply
818
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
1
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5
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3.1k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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6
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2.3k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.3 years ago Weiqian ▴ 10
0
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0
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604
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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
3.3 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 3.3 years ago by 53k • written 3.3 years ago by ▴ 10
0
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2
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1.4k
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IsoformSwitchAnalyzeR package on mouse data
rnaseq IsoformSwitchAnalyzeR
updated 3.2 years ago by ▴ 120 • written 3.3 years ago by • 0
0
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1
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1.4k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.3 years ago Jenny Drnevich ★ 2.0k
5
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6
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2.7k
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Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.3 years ago Yang Shi ▴ 10
1
vote
5
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1.4k
views
DeSeq2 Matched Analysis
RNASeq DESeq2
3.3 years ago Andrea • 0
3
votes
4
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1.5k
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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
3.3 years ago Yang Shi ▴ 10
1
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2
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3.0k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.3 years ago ClaudiaE • 0
1
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0
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908
views
Which algorithm would you use for the cell-cell communication analysis of bulk RNA seq datasets?
RNASeq
3.3 years ago curiousmind007 ▴ 10
3
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4
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3.6k
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Why Negative value from GSVA
GSVA RNASeq edgeR
3.3 years ago Yang Shi ▴ 10
5
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8
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27k
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Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 15 months ago by ▴ 60 • written 3.4 years ago by ▴ 30
2
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2
replies
1.4k
views
Can't load UCSC transcript IDs
RNASeq
updated 3.4 years ago by ★ 4.1k • written 3.4 years ago by • 0
2
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4
replies
2.3k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 7 months ago by 43k • written 3.4 years ago by ▴ 10
3
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3
replies
1.4k
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
1
reply
964
views
lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
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1
reply
770
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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1
reply
1.1k
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
vote
1
reply
1.2k
views
NOIseq Probability column
RNAseq RNASeqData NOISeq
3.4 years ago Pratibha ▴ 10
9
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3
replies
9.6k
views
Limma vs deseq2 results
limma RNASeq R
3.4 years ago k___ ▴ 30
3
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3
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2.4k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
3
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9
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3.2k
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 2.9 years ago by • 0 • written 3.5 years ago by ▴ 20
1
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2
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2.2k
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 3.5 years ago by ▴ 10
1
vote
1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
1
vote
2
replies
1.7k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
3
votes
11
replies
4.3k
views
RNA-seq: compare two technical replicates
RNASeq
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 20
0
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2
replies
997
views
edgeR
rnaseq edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
0
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3
replies
6.7k
views
Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
5
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6
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4.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
3.6 years ago Alan • 0
0
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0
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1.2k
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.6 years ago chiwut.wong • 0
0
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0
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1.2k
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.6 years ago OST • 0
6
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4
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4.3k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
3.6 years ago Al90 ▴ 10
0
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7
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2.1k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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1
reply
1.1k
views
Rtracklayer
rtracklayer RNASeq gff
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
reply
1.2k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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3
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1.3k
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
2
replies
2.9k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3.6 years ago by • 0 • written 9.2 years ago by ▴ 50
0
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0
replies
1.1k
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3.6 years ago treebig44 ▴ 40
1
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0
replies
871
views
Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery RNASeq
3.6 years ago Liliian • 0
0
votes
0
replies
4.2k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.6 years ago Raito92 ▴ 60
1,409 results • Page 5 of 29
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Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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