Showing : mirna • reset
1
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603
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
1
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4
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656
views
How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
11 months ago • updated 8 months ago richardallenfriedmanbrooklyn ▴ 20
1
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1
reply
747
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 14 months ago by 50k • written 14 months ago by • 0
6
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6
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1.4k
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
17 months ago Sara ▴ 10
1
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3
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1.6k
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miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 22 months ago by 41k • written 22 months ago by • 0
0
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1
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584
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miRNA analysis with DESeq2
mirna DESeq2
updated 23 months ago by 41k • written 23 months ago by • 0
2
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2
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921
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edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
24 months ago • updated 23 months ago Sarah • 0
0
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3
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839
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DESEQ PCA
DESeq2 miRNA
updated 2.7 years ago by ★ 1.3k • written 2.7 years ago by • 0
0
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1
reply
874
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How to calculate high and low tumor mutational burden
SomaticMutation miRNA
updated 2.9 years ago by ★ 4.0k • written 2.9 years ago by ▴ 20
0
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1
reply
820
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mircomb analysis from deg's list
mircomb mrna mirna degs interaction
3.8 years ago andreia ▴ 10
0
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2
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1.2k
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Very high threshold for independent filtering
deseq2 mirna independent filtering
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
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5
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1.4k
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Hill shape p-value histogram after differential miRNA expression analysis with DESeq2
deseq2 mirna fdrtool
updated 5.2 years ago by ★ 3.3k • written 5.2 years ago by • 0
1
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8
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2.5k
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 5.6 years ago by ★ 6.8k • written 5.6 years ago by ▴ 20
1
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2
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1.1k
views
Whether "read_counts_miRNA" or "reads_per_million_miRNA" to use for DE expression analysis using DeSeq2
tcgadownload deseq2 mirna normalization
updated 5.9 years ago by ▴ 120 • written 5.9 years ago by • 0
0
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0
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1.2k
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miR2Pathway Finite Observations
pathway analysis mirna parallel
6.1 years ago genomic8328 ▴ 10
2
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0
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1.2k
views
Job: PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna riboseq smallrna differential gene expression Job
6.1 years ago Andy Lynch ▴ 120
0
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1
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1.2k
views
Best way to analyze multiple treatments using DESeq2?
deseq2 rna-seq mirna
updated 6.1 years ago by 41k • written 6.1 years ago by • 0
0
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0
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1.2k
views
Custom graphNEL object for pathview
pathview mirintegrator miRNA
6.5 years ago drowsygoat ▴ 30
6
votes
4
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2.6k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray mirna oligo package pdinfobuilder pd.mirna
updated 4.4 years ago by ▴ 10 • written 6.9 years ago by ▴ 20
4
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3
replies
3.7k
views
EdgeR on miRNA data
edger miRNA
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
0
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4
replies
4.5k
views
miRNA-seq data analysis
miRNA mirna-seq
updated 7.1 years ago by ▴ 250 • written 7.1 years ago by • 0
0
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0
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1.5k
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miRNA target prediction tool(package) using R
mirna prediction target
7.2 years ago Adam • 0
1
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1
reply
1.0k
views
miRNA normalization for large amount of samples using LVSmiRNA
mirna normalization
7.5 years ago • updated 7.3 years ago carleshf ▴ 10
2
votes
5
replies
1.7k
views
miRNA Probe IDs
mirna microarray mirbase.db
updated 7.5 years ago by ★ 1.5k • written 7.5 years ago by • 0
1
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2
replies
1.8k
views
Rsubread align for miRNAseq?
rsubread miRNA
updated 7.6 years ago by ★ 3.6k • written 7.6 years ago by ▴ 620
0
votes
2
replies
949
views
Differential expression of one group agains all samples
deseq2 mirna differential gene expression
updated 7.6 years ago by ▴ 680 • written 7.6 years ago by ▴ 10
0
votes
2
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2.1k
views
TPM for miRNA tags
mirna
7.6 years ago manoharankumar01 • 0
0
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0
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1.3k
views
Normalizing miRNA-1_0 and miRNA-1_0_2Xgain type arrays simultaneously
mirna microarray normalization
7.6 years ago arisarkar88 ▴ 40
3
votes
6
replies
4.4k
views
Affymetrix miRNA 4.0 Normalization and Analysis
R Limma microarray miRNA
updated 3.0 years ago by ▴ 10 • written 8.2 years ago by ▴ 90
4
votes
6
replies
2.7k
views
limma: within-array duplicates correlation
limma mirna microarray
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
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0
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1.4k
views
get precursor mirna from mature mirna
bioconductor mirna mir mirbase.db
8.3 years ago C T ▴ 140
3
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4
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1.8k
views
Network generation from adjacency matrix of zeroes and ones
R adjacency matrix mirna
8.4 years ago alptaciroglu ▴ 50
0
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0
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1.5k
views
miRNA 3D-Gene chips Toray
Toray 3D-Gene miRNA limma
8.5 years ago santi.cabellos ▴ 10
0
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0
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1.0k
views
targetScan R errors
targetscan R error handling miRNA
8.6 years ago alptaciroglu ▴ 50
1
vote
5
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1.5k
views
normalization of a miRNA microarray
normalization vsn eximir microarray miRNA
updated 8.6 years ago by ★ 13k • written 8.6 years ago by ▴ 50
1
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1
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1.2k
views
How can get the GO and KEGG miRNA microarray Agilent?
go kegg limma microarray mirna
8.6 years ago santi.cabellos ▴ 10
2
votes
5
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2.0k
views
Problems with "read.agiMicroRna"
read.agiMicroRna agilent limma microarray mirna
updated 8.6 years ago by ▴ 30 • written 8.6 years ago by ▴ 10
4
votes
2
replies
2.2k
views
Detect global differences in miRNA expression between tumor and normal using spike-ins
edger limma mirna sequencing
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 40
2
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5
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3.0k
views
miRNA expression analysis : annotation
miRNA annotation affymetrixchip
9.0 years ago aswathym ▴ 10
0
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0
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996
views
Invitation Research Collaborations
cancer microarray mirna sequencing
9.0 years ago alexandru.floares • 0
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0
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1.8k
views
News: RNAseq data analysis courses: Torino (Italy) : Beginner course March 17-19 2015 & Advance Course April 14-16 2015
rnaseq mirna onechannelgui chimera News
9.3 years ago raffaele calogero ▴ 500
3
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1
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1.3k
views
Bioinformatics researching Schizophrenia
miRNA
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by ★ 13k
0
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5
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1.9k
views
Using custom CDF with 'make.cdf.env'
miRNA cdf probe miRNA cdf probe
updated 9.7 years ago by ▴ 130 • written 9.7 years ago by ★ 13k
6
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2
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1.9k
views
Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?
miRNA cdf probe limma miRNA cdf probe limma
updated 9.6 years ago by 50k • written 9.7 years ago by ★ 13k
0
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0
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4.0k
views
cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Sequencing miRNA edgeR Sequencing miRNA edgeR
9.9 years ago Gordon Smyth 50k
0
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0
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1.1k
views
total count filter cutoff (edgeR)
miRNA edgeR miRNA edgeR
9.9 years ago Daniel ▴ 10
0
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0
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1.2k
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QuasR for miRNA
miRNA QuasR miRNA QuasR
9.9 years ago Michael Stadler ▴ 350
0
votes
4
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1.6k
views
combat error message
miRNA Normalization affy miRNA Normalization affy
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 850
0
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0
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1.0k
views
ComBat error message, thanks
miRNA Normalization affy miRNA Normalization affy
10.0 years ago Guan ▴ 20
0
votes
2
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1.4k
views
About ChIPpeakAnno
miRNA ChIPpeakAnno miRNA ChIPpeakAnno
updated 10.0 years ago by ★ 4.3k • written 10.0 years ago by ▴ 330
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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