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19
votes
3
answers
27k
views
14 follow
3
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Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
rna-seq heatmap written 7.7 years ago by KJ Lim130 • updated 7.7 years ago by Damian Kao15k
44
votes
4
answers
26k
views
4
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I would like to add gene names to a volcano plot obtained from DEseq2
R deseq2 rna-seq written 3.9 years ago by ta_awwad260 • updated 2.1 years ago by Kevin Blighe60k
32
votes
2
answers
26k
views
5 follow
2
answers
Calculating TPM from featureCounts output
rna-seq written 4.4 years ago by nash.claire390 • updated 16 months ago by janzrimec0
36
votes
2
answers
26k
views
2
answers
Recommended cutoff for FDR - 0.05 or 0.1
R rna-seq written 3.8 years ago by aggregatibacter140 • updated 3.8 years ago by daniel.dvorkin260
22
votes
4
answers
25k
views
4
answers
How to import huge .csv files in R studio?
R rna-seq written 3.6 years ago by krushnach80750 • updated 3.6 years ago by Ron990
18
votes
2
answers
25k
views
2
answers
what is the difference between GRCh37 and hg19 ?
genome assembly alignment rna-seq written 5.5 years ago by jack800 • updated 5 months ago by Kevin Blighe60k
49
votes
1
answer
24k
views
1
answer
Paired-end reads - what is what?
paired-end rna-seq sequencing written 5.0 years ago by darxsys190 • updated 5.0 years ago by thackl2.8k
57
votes
1
answer
24k
views
10 follow
1
answer
12
votes
1
answer
23k
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8 follow
1
answer
44
votes
2
answers
23k
views
32 follow
2
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Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
rna-seq written 5.9 years ago by thisismytest3023170 • updated 5.1 years ago by juara10
14
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2
answers
23k
views
2
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hg38 annotation file (gtf) UCSC format
alignment rna-seq written 4.4 years ago by dina.hesham139120 • updated 3.4 years ago by inambioinfo100
19
votes
1
answer
22k
views
9 follow
1
answer
Trimmomatic: Trimming only custom adapter sequences
next-gen rna-seq sequencing written 5.9 years ago by lewis.stevens0780 • updated 5.9 years ago by Dan D7.1k
17
votes
8
answers
22k
views
6 follow
8
answers
how to unzip the files in batch?
next-gen alignment rna-seq snp written 5.1 years ago by flavobacteria40 • updated 2.1 years ago by saraholiver3070
70
votes
1
answer
22k
views
48 follow
1
answer
PCA plot from read count matrix from RNA-Seq
pca rna-seq written 2.6 years ago by rachel.kubik12120 • updated 12 months ago by mayankkaashyap30
90
votes
3
answers
22k
views
67 follow
3
answers
Tutorial: Guide to TCGA data
cancer tutorial tcga rna-seq tools clinical written 4.3 years ago by Jordan Anaya1.1k • updated 3.5 years ago by ewre220
10
votes
2
answers
22k
views
2
answers
generating genome indexes with STAR
star rna-seq written 4.0 years ago by snp8750 • updated 3.5 years ago by aleferna0
13
votes
2
answers
22k
views
2
answers
What does "isoform" and "transcript variant" differ by definition?
genome rna-seq written 5.4 years ago by wangyi2412220 • updated 5.4 years ago by cdsouthan1.8k
109
votes
1
answer
22k
views
93 follow
1
answer
28
votes
2
answers
22k
views
2
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RNA-seq: Explain STAR quantMode geneCounts values
star rna-seq differential expression written 3.6 years ago by williantafsilva210 • updated 2.2 years ago by Tao370
7
votes
3
answers
21k
views
3
answers
Error: could not find function "heatmap.2"
deseq2 rna-seq heatmap written 5.9 years ago by madkitty600 • updated 5.9 years ago by Alex Reynolds30k
61
votes
3
answers
21k
views
58 follow
3
answers
Tutorial: Rna-Seq Review Papers
tutorial papers rna-seq written 7.8 years ago by Istvan Albert ♦♦ 84k • updated 4.3 years ago by art.matysik0
17
votes
4
answers
21k
views
7 follow
4
answers
Rna-Seq Data In Public Database
rna-seq written 7.7 years ago by camelbbs670 • updated 6.9 years ago by alaincoletta160
15
votes
2
answers
21k
views
10 follow
2
answers
Normalization Method In Comparing Differential Gene Expression
rna-seq written 7.6 years ago by camelbbs670 • updated 22 months ago by ra296720
9
votes
2
answers
21k
views
2
answers
Bioconductor : Setting local install directory for packages
bioconductor install rna-seq written 4.7 years ago by irritable_phd_syndrom70 • updated 4.4 years ago by charco50
14
votes
3
answers
20k
views
5 follow
3
answers
TCGA RNA-Seq Data: RSEM and RPKM
rpkm tcga rsem tcga-assembler rna-seq written 5.6 years ago by NetunoPonc√£160 • updated 3.7 years ago by Biostar ♦♦ 20
19
votes
1
answer
20k
views
10 follow
1
answer
Deseq, Edger And Cuffdiff - Different Result
differential expression analysis rna-seq written 8.0 years ago by Nicolas Rosewick8.8k • updated 7.8 years ago by Arun2.3k
7
votes
2
answers
20k
views
10 follow
2
answers
RNAseq expression data log2 transformed has negative values.
rna-seq written 6.0 years ago by juncheng200 • updated 6.0 years ago by dariober11k
23
votes
1
answer
19k
views
1
answer
62
votes
3
answers
19k
views
56 follow
3
answers
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
bioconductor fpkm forum rna-seq tutorial written 6.6 years ago by Irsan7.1k • updated 2.3 years ago by lhdcsu30
47
votes
6
answers
19k
views
20 follow
6
answers
Remove mitochondrial reads from BAM files
bam samtools rna-seq awk written 5.4 years ago by enricoferrero800 • updated 2.6 years ago by Simply Bioinformatics170
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