Showing : RNAseq • reset
0
votes
0
replies
711
views
how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
3.1 years ago marymshahi2021 • 0
0
votes
2
replies
2.4k
views
maSigPro: how to extract the genes in the same cluster
rnaseq
updated 3.1 years ago by • 0 • written 9.5 years ago by ▴ 10
1
vote
2
replies
768
views
how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
votes
1
reply
1.4k
views
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
votes
8
replies
3.0k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 3.2 years ago by ▴ 10
0
votes
2
replies
2.6k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 3.2 years ago by ▴ 270 • written 3.3 years ago by • 0
0
votes
0
replies
790
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.2 years ago osieman52 • 0
4
votes
5
replies
3.4k
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 3.2 years ago by ▴ 10
1
vote
1
reply
800
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
5
replies
3.1k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
6
replies
2.2k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.2 years ago Weiqian ▴ 10
0
votes
0
replies
591
views
Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
3.2 years ago Pang • 0
1
vote
1
reply
1.3k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 10
0
votes
2
replies
1.4k
views
IsoformSwitchAnalyzeR package on mouse data
rnaseq IsoformSwitchAnalyzeR
updated 3.2 years ago by ▴ 120 • written 3.2 years ago by • 0
0
votes
1
reply
1.4k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.2 years ago Jenny Drnevich ★ 2.0k
5
votes
6
replies
2.6k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.2 years ago Yang Shi ▴ 10
1
vote
5
replies
1.3k
views
DeSeq2 Matched Analysis
RNASeq DESeq2
3.2 years ago Andrea • 0
3
votes
4
replies
1.5k
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.2 years ago Yang Shi ▴ 10
1
vote
2
replies
3.0k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.2 years ago ClaudiaE • 0
1
vote
0
replies
887
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
votes
4
replies
3.5k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
3.3 years ago Yang Shi ▴ 10
5
votes
8
replies
27k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 14 months ago by ▴ 60 • written 3.3 years ago by ▴ 30
2
votes
2
replies
1.3k
views
Can't load UCSC transcript IDs
RNASeq
updated 3.3 years ago by ★ 4.1k • written 3.3 years ago by • 0
2
votes
4
replies
2.3k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 6 months ago by 43k • written 3.3 years ago by ▴ 10
3
votes
3
replies
1.3k
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
1
reply
949
views
lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
1
reply
754
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
1
reply
1.1k
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
1
reply
1.1k
views
NOIseq Probability column
RNAseq RNASeqData NOISeq
3.3 years ago Pratibha ▴ 10
9
votes
3
replies
9.5k
views
Limma vs deseq2 results
limma RNASeq R
3.4 years ago k___ ▴ 30
3
votes
3
replies
2.4k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
3
votes
9
replies
3.2k
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 2.8 years ago by • 0 • written 3.4 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 3.4 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
vote
2
replies
1.7k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
3
votes
11
replies
4.3k
views
RNA-seq: compare two technical replicates
RNASeq
updated 3.4 years ago by 53k • written 3.5 years ago by ▴ 20
0
votes
2
replies
985
views
edgeR
rnaseq edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
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 3.5 years ago by ★ 1.4k • written 3.5 years ago by • 0
5
votes
6
replies
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
3.5 years ago Alan • 0
0
votes
0
replies
1.2k
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.5 years ago chiwut.wong • 0
0
votes
0
replies
1.1k
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.5 years ago OST • 0
6
votes
4
replies
4.3k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
3.5 years ago Al90 ▴ 10
0
votes
7
replies
2.0k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
1
reply
1.0k
views
Rtracklayer
rtracklayer RNASeq gff
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
1
reply
1.2k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
3
replies
1.3k
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
2
replies
2.9k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3.5 years ago by • 0 • written 9.1 years ago by ▴ 50
0
votes
0
replies
1.0k
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3.5 years ago treebig44 ▴ 40
1
vote
0
replies
854
views
Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery RNASeq
3.5 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
3.5 years ago Raito92 ▴ 60
1,409 results • Page 5 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Locations • All
Seattle, WA, United States, 59 minutes ago
United States, 1 hour ago
UK/Cambridge, 1 hour ago
San Diego, 1 hour ago
Denmark, 1 hour ago
Traffic: 768 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6