Showing : miRNA • reset
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
14 months ago Wending • 0
1
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4
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1.0k
views
How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
20 months ago • updated 17 months ago richardallenfriedmanbrooklyn ▴ 30
1
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1
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1.0k
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 23 months ago by 52k • written 23 months ago by • 0
6
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6
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1.8k
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
2.1 years ago Sara ▴ 20
1
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3
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2.3k
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miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
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1
reply
762
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miRNA analysis with DESeq2
mirna DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
2
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2
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1.3k
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edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
2.7 years ago Sarah • 0
0
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3
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1.1k
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DESEQ PCA
DESeq2 miRNA
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
0
votes
1
reply
1.1k
views
How to calculate high and low tumor mutational burden
SomaticMutation miRNA
updated 3.6 years ago by ★ 4.6k • written 3.6 years ago by ▴ 20
0
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1
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1.6k
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edgeR on microRNA data
miRNA edgeR miRNA edgeR
updated 3.6 years ago by 52k • written 13.3 years ago by ▴ 50
0
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1
reply
1.0k
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mircomb analysis from deg's list
mircomb mrna mirna degs interaction
4.5 years ago andreia ▴ 10
6
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4
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3.0k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray mirna oligo package pdinfobuilder pd.mirna
updated 5.1 years ago by ▴ 10 • written 7.6 years ago by ▴ 20
0
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2
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1.5k
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Very high threshold for independent filtering
deseq2 mirna independent filtering
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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5
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1.7k
views
Hill shape p-value histogram after differential miRNA expression analysis with DESeq2
deseq2 mirna fdrtool
updated 5.9 years ago by ★ 3.4k • written 5.9 years ago by • 0
1
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8
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2.9k
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Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 20
1
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2
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1.3k
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Whether "read_counts_miRNA" or "reads_per_million_miRNA" to use for DE expression analysis using DeSeq2
tcgadownload deseq2 mirna normalization
updated 6.5 years ago by ▴ 140 • written 6.5 years ago by • 0
0
votes
0
replies
1.4k
views
miR2Pathway Finite Observations
pathway analysis mirna parallel
6.8 years ago genomic8328 ▴ 10
2
votes
0
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1.4k
views
Job: PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna riboseq smallrna differential gene expression Job
6.8 years ago Andy Lynch ▴ 120
0
votes
1
reply
1.4k
views
Best way to analyze multiple treatments using DESeq2?
deseq2 rna-seq mirna
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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0
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1.4k
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Custom graphNEL object for pathview
pathview mirintegrator miRNA
7.2 years ago drowsygoat ▴ 30
4
votes
3
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4.3k
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EdgeR on miRNA data
edger miRNA
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
4
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5.0k
views
miRNA-seq data analysis
miRNA mirna-seq
updated 7.8 years ago by ▴ 260 • written 7.8 years ago by • 0
0
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0
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1.7k
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miRNA target prediction tool(package) using R
mirna prediction target
7.8 years ago Adam • 0
1
vote
1
reply
1.2k
views
miRNA normalization for large amount of samples using LVSmiRNA
mirna normalization
8.2 years ago • updated 8.0 years ago carleshf ▴ 10
2
votes
5
replies
2.0k
views
miRNA Probe IDs
mirna microarray mirbase.db
updated 8.2 years ago by ★ 1.5k • written 8.2 years ago by • 0
1
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2
replies
2.0k
views
Rsubread align for miRNAseq?
rsubread miRNA
updated 8.2 years ago by ★ 3.6k • written 8.2 years ago by ▴ 620
0
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2
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1.1k
views
Differential expression of one group agains all samples
deseq2 mirna differential gene expression
updated 8.3 years ago by ▴ 690 • written 8.3 years ago by ▴ 10
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2
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2.3k
views
TPM for miRNA tags
mirna
8.3 years ago manoharankumar01 • 0
0
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0
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1.4k
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Normalizing miRNA-1_0 and miRNA-1_0_2Xgain type arrays simultaneously
mirna microarray normalization
8.3 years ago arisarkar88 ▴ 40
3
votes
6
replies
5.0k
views
Affymetrix miRNA 4.0 Normalization and Analysis
R Limma microarray miRNA
updated 3.6 years ago by ▴ 10 • written 8.9 years ago by ▴ 90
4
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6
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3.0k
views
limma: within-array duplicates correlation
limma mirna microarray
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
0
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0
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1.5k
views
get precursor mirna from mature mirna
bioconductor mirna mir mirbase.db
9.0 years ago C T ▴ 140
3
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4
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2.1k
views
Network generation from adjacency matrix of zeroes and ones
R adjacency matrix mirna
9.1 years ago alptaciroglu ▴ 50
0
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0
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1.6k
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miRNA 3D-Gene chips Toray
Toray 3D-Gene miRNA limma
9.2 years ago santi.cabellos ▴ 10
0
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0
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1.2k
views
targetScan R errors
targetscan R error handling miRNA
9.2 years ago alptaciroglu ▴ 50
1
vote
5
replies
1.8k
views
normalization of a miRNA microarray
normalization vsn eximir microarray miRNA
updated 9.3 years ago by ★ 13k • written 9.3 years ago by ▴ 50
1
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1
reply
1.4k
views
How can get the GO and KEGG miRNA microarray Agilent?
go kegg limma microarray mirna
9.3 years ago santi.cabellos ▴ 10
2
votes
5
replies
2.2k
views
Problems with "read.agiMicroRna"
read.agiMicroRna agilent limma microarray mirna
updated 9.3 years ago by ▴ 30 • written 9.3 years ago by ▴ 10
4
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2
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2.5k
views
Detect global differences in miRNA expression between tumor and normal using spike-ins
edger limma mirna sequencing
updated 9.5 years ago by ★ 28k • written 9.5 years ago by ▴ 40
2
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5
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3.2k
views
miRNA expression analysis : annotation
miRNA annotation affymetrixchip
9.7 years ago aswathym ▴ 10
0
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0
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1.1k
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Invitation Research Collaborations
cancer microarray mirna sequencing
9.7 years ago alexandru.floares • 0
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0
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1.9k
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News: RNAseq data analysis courses: Torino (Italy) : Beginner course March 17-19 2015 & Advance Course April 14-16 2015
rnaseq mirna onechannelgui chimera News
10.0 years ago raffaele calogero ▴ 500
6
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2
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2.1k
views
Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?
miRNA cdf probe limma miRNA cdf probe limma
updated 10.3 years ago by 52k • written 10.4 years ago by ★ 13k
3
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1
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1.5k
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Bioinformatics researching Schizophrenia
miRNA
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by ★ 13k
0
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5
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2.2k
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Using custom CDF with 'make.cdf.env'
miRNA cdf probe miRNA cdf probe
updated 10.4 years ago by ▴ 130 • written 10.4 years ago by ★ 13k
0
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0
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4.3k
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cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Sequencing miRNA edgeR Sequencing miRNA edgeR
10.5 years ago Gordon Smyth 52k
0
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0
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1.2k
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total count filter cutoff (edgeR)
miRNA edgeR miRNA edgeR
10.5 years ago Daniel ▴ 10
0
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0
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1.4k
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QuasR for miRNA
miRNA QuasR miRNA QuasR
10.6 years ago Michael Stadler ▴ 350
0
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4
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1.8k
views
combat error message
miRNA Normalization affy miRNA Normalization affy
updated 10.6 years ago by ★ 13k • written 10.7 years ago by ▴ 870
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0
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1.2k
views
ComBat error message, thanks
miRNA Normalization affy miRNA Normalization affy
10.7 years ago Guan ▴ 20
50 results • Page 1 of 1
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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