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3
votes
7
replies
8.1k
views
How does edgeR do ERCC spike-in normalization?
RNA-Seq R
updated 16 months ago by 43k • written 7.6 years ago by ▴ 510
5
votes
2
replies
3.1k
views
How to calculate the similairty of two protein structures in .pdb file format or how to measure the accuracy of alphafold predicted protein structure?
alphafold structure protein
updated 2.5 years ago by • 0 • written 2.7 years ago by ▴ 510
2
votes
7
replies
4.3k
views
6 follow
How to remove samples with no genotypes from vcf
VCF
updated 18 months ago by ▴ 40 • written 2.9 years ago by ▴ 510
2
votes
2
replies
2.0k
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS power
3.0 years ago by moxu ▴ 510
0
votes
1
reply
681
views
How Did 1000 Genomes Project Enroll Samples To Populations
genomes population
3.8 years ago by moxu ▴ 510
0
votes
0
replies
1.0k
views
How to build an imputation reference panel from a fasta file of many samples
sequencing SNP alignment Assembly
4.9 years ago by moxu ▴ 510
2
votes
8
replies
6.5k
views
8 follow
Step by step instructions to phase with Eagle?
snp genome software error
updated 3.1 years ago by • 0 • written 7.7 years ago by ▴ 510
2
votes
1
reply
1.3k
views
How to convert Merlin phased result files to vcf
genome snp assembly software error
5.7 years ago by moxu ▴ 510
1
vote
0
replies
1.7k
views
How to resolve kinship with the software "king" using GWAS genotyping data?
SNP
5.8 years ago by moxu ▴ 510
3
votes
8
replies
4.3k
views
Can someone please help me run any GATK4 pipeline?
software error sequencing next-gen snp
updated 2.1 years ago by ▴ 40 • written 5.9 years ago by ▴ 510
2
votes
4
replies
1.4k
views
Where to find information on LD ~ distance?
SNP genome
5.9 years ago by moxu ▴ 510
4
votes
2
replies
2.9k
views
GATK4 local computing workflow
software error genome next-gen sequencing
updated 6.0 years ago by ★ 1.2k • written 6.0 years ago by ▴ 510
1
vote
5
replies
1.4k
views
How can I make RSEM to align ChIPseq signal to the nearest gene?
ChIP-Seq next-gen sequencing alignment gene
updated 6.0 years ago by 20 • written 6.5 years ago by ▴ 510
0
votes
1
reply
931
views
Why mach1 is not imputing SNPs?
SNP software error
6.0 years ago by moxu ▴ 510
0
votes
0
replies
1.0k
views
mach1 phasing reference Haplotypes file(s)
SNP software error
6.0 years ago by moxu ▴ 510
4
votes
4
replies
2.8k
views
Merlin format, Mach, Plink, Plink2, and best practices of snp imputation
SNP software error
6.0 years ago by moxu ▴ 510
5
votes
2
replies
2.1k
views
How to map probeset associated statistics to gene statistics in microarray differential expression analysis?
gene R RNA-Seq
updated 6.1 years ago by 87k • written 6.1 years ago by ▴ 510
3
votes
6
replies
1.8k
views
paired-end, single-end, polyA tail, 500bp, and removal of RNA genes
next-gen rna-seq
6.2 years ago by moxu ▴ 510
5
votes
4
replies
4.8k
views
microarray, RNAseq, CEL, edgeR, etc. for DGE analysis
RNA-Seq microarray gene
updated 6.2 years ago by 87k • written 6.2 years ago by ▴ 510
0
votes
4
replies
1.6k
views
mixing R ggplot2 with old style plot
R software error SNP
updated 6.3 years ago by 14k • written 6.3 years ago by ▴ 510
1
vote
0
replies
1.2k
views
edgeR and contrast
RNA-Seq next-gen R
6.4 years ago by moxu ▴ 510
7
votes
8
replies
2.1k
views
edgeR analysis dilemma -- what samples to include
RNA-Seq software error R next-gen
updated 6.4 years ago by 13k • written 6.4 years ago by ▴ 510
3
votes
3
replies
4.4k
views
heatmap.2 row clustering does not look right
RNA-Seq software error next-gen R
updated 6.4 years ago by 87k • written 6.4 years ago by ▴ 510
2
votes
4
replies
2.8k
views
rsem-prepare-reference and mouse mm9 genome reference files
RNA-Seq R genome next-gen alignment
updated 6.4 years ago by ▴ 40 • written 6.4 years ago by ▴ 510
2
votes
4
replies
2.8k
views
How to install a bioconductor package RMySQL and specify R parameters
R software error next-gen ChIP-Seq
6.5 years ago by moxu ▴ 510
0
votes
0
replies
706
views
How does RSEM allocate ChIPseq signals to genes?
ChIP-Seq Assembly gene next-gen
6.5 years ago by moxu ▴ 510
8
votes
10
replies
5.1k
views
snpEff inappropriate interpretation of variants?
RNA-Seq software error alignment variant calling
updated 6.7 years ago by ★ 1.8k • written 6.8 years ago by ▴ 510
7
votes
1
reply
1.0k
views
Does CAG code for Valine?
gene sequencing
updated 6.8 years ago by 161k • written 6.8 years ago by ▴ 510
3
votes
3
replies
1.5k
views
functional variant discovery after GATK variant calling
gene SNP genome
updated 6.8 years ago by ▴ 990 • written 6.8 years ago by ▴ 510
2
votes
3
replies
2.1k
views
why use partial correlation for gene-gene network construction
R gene rna-seq
6.9 years ago by moxu ▴ 510
0
votes
0
replies
1.1k
views
partial correlation and conditions
R rna-seq
6.9 years ago by moxu ▴ 510
4
votes
13
replies
4.3k
views
edgeR again: can you AND multiple conditions for analysis?
R RNA-Seq
updated 6.9 years ago by 104k • written 6.9 years ago by ▴ 510
1
vote
3
replies
4.1k
views
multivariate analysis of RNA-seq
RNA-Seq R next-gen
updated 7.0 years ago by 20 • written 7.1 years ago by ▴ 510
0
votes
5
replies
2.9k
views
Gene-Gene interaction Network Analysis and Visualization Software
R RNA-Seq gene
updated 7.0 years ago by 27k • written 7.0 years ago by ▴ 510
1
vote
1
reply
2.1k
views
edgeR normalization and partial correlation matrix calculation
next-gen rna-seq R gene
7.0 years ago by moxu ▴ 510
5
votes
8
replies
12k
views
How many genes to include for a GSEA analysis
rna-seq next-gen gene
updated 2.7 years ago by • 0 • written 7.0 years ago by ▴ 510
0
votes
3
replies
13k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R rna-seq next-gen
7.0 years ago by moxu ▴ 510
9
votes
13
replies
3.4k
views
[edgeR usage] Comparing categories of fewer input variables for differential gene expression
R RNA-Seq next-gen
7.1 years ago by moxu ▴ 510
2
votes
12
replies
3.8k
views
[edgeR Usage] How does edgeR handle multivariate gene expression analysis
RNA-Seq R next-gen
7.1 years ago by moxu ▴ 510
6
votes
12
replies
3.0k
views
How does one refer gene gene network from a partial correlation matrix?
R RNA-Seq gene
7.1 years ago by moxu ▴ 510
0
votes
2
replies
1.5k
views
How to analyze gene expression datasets with rich controls
gene R RNA-Seq
updated 7.2 years ago by ▴ 180 • written 7.2 years ago by ▴ 510
7
votes
5
replies
4.0k
views
How to programmatically retrieve the p-value of the slope of a linear regression using either R or perl
R
updated 7.2 years ago by ▴ 20 • written 7.2 years ago by ▴ 510
0
votes
10
replies
2.1k
views
How to compare two groups of 3 samples
R gene
updated 7.2 years ago by ▴ 250 • written 7.2 years ago by ▴ 510
1
vote
2
replies
1.6k
views
The best way to correlate some genome wide signal to histone modification signal
RNA-Seq ChIP-Seq next-gen
updated 7.2 years ago by ▴ 690 • written 7.2 years ago by ▴ 510
4
votes
7
replies
3.7k
views
bigWig to bigBed conversion
next-gen genome sequence
7.2 years ago by moxu ▴ 510
0
votes
5
replies
1.6k
views
comparing two tracks over intervals on the genome
next-gen alignment software error
updated 7.4 years ago by 35k • written 7.4 years ago by ▴ 510
16
votes
18
replies
27k
views
how to avoid R automatically converting strings to numbers
R software error
updated 7.5 years ago by ★ 2.0k • written 7.5 years ago by ▴ 510
2
votes
11
replies
3.6k
views
edgeR artifacts on p-value and/or fold change?
rna-seq RSEM edgeR
7.5 years ago by moxu ▴ 510
1
vote
7
replies
3.7k
views
edgeR Gene Ontology Analysis always returns the same list of pathways
software error RNA-Seq next-gen gene
7.6 years ago by moxu ▴ 510
2
votes
5
replies
6.0k
views
RSEM error: RSEM can not recognize reference sequence name chrM!
software error next-gen alignment RNA-Seq
7.6 years ago by moxu ▴ 510
60 results • Page 1 of 2
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