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How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR RNA-seq Batch RSEM effect
updated 13 days ago by ★ 7.9k • written 14 days ago by ▴ 170
0
votes
0
replies
332
views
When I want to compare two groups at multiple time points in scRNA-seq datasets, the criteria for the genes to be analyzed
Seurat scRNA-seq
25 days ago by Apprentice ▴ 170
0
votes
4
replies
1.0k
views
Commands for processing mixed 4-sample scRNA-seq data with cellranger
Cellranger scRNA-seq Chromium
3 months ago by Apprentice ▴ 170
2
votes
7
replies
1.2k
views
Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat?
scRNA-seq CellRanger hdWGCNA Seurat
3 months ago by Apprentice ▴ 170
0
votes
2
replies
486
views
Can I use FDR twice for multiple correction in a two-stage study using omics data.
statistical omics-data testing RNA-seq
4 months ago by Apprentice ▴ 170
5
votes
15
replies
7.2k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq IGV mapping
updated 13 months ago by • 0 • written 5.8 years ago by ▴ 170
0
votes
3
replies
1.1k
views
Calculation of λ1000 for a continuous trait
SNP GWAS inflation
13 months ago by Apprentice ▴ 170
7
votes
15
replies
2.2k
views
6 follow
I would like to exclude rRNA in RSEM and quantify other genes.
STAR RNA-seq RSEM
updated 14 months ago by ★ 7.3k • written 15 months ago by ▴ 170
0
votes
2
replies
675
views
I would like to add a human gene sequence to a mouse reference genome
reference-genome mouse RNA-seq
updated 15 months ago by 45k • written 15 months ago by ▴ 170
0
votes
0
replies
467
views
If the names of miRNAs are the same for different species, are they the same sequence?
miRNA
16 months ago by Apprentice ▴ 170
0
votes
0
replies
363
views
Method for detecting X-chromosome aneuploidy from SNP array data
SNP aneuploidies
18 months ago by Apprentice ▴ 170
2
votes
3
replies
1.4k
views
LD score table for East Asians used for BOLT-LMM
BOLT-LMM SNP LDSC
updated 19 months ago by 4.9k • written 20 months ago by ▴ 170
2
votes
2
replies
757
views
Is it possible to detect fusion genes by either stranded or unstranded RNA-seq?
RNA-seq STAR-Fusion
20 months ago by Apprentice ▴ 170
0
votes
0
replies
456
views
PLINK format file for BOLT-LMM
BOLT-LMM SNP
20 months ago by Apprentice ▴ 170
5
votes
3
replies
1.7k
views
RSEM uses different gene lengths for each sample.
STAR RNA-seq RSEM
20 months ago by Apprentice ▴ 170
3
votes
8
replies
1.9k
views
Is RSEM required for RNA-seq data analysis using STAR and edgeR?
edgeR RNA-seq STAR
21 months ago by Apprentice ▴ 170
0
votes
0
replies
434
views
Popcorn using SNPs with extremely low P-value
Popcorn SNP
22 months ago by Apprentice ▴ 170
2
votes
1
reply
854
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2 SNP
22 months ago by Apprentice ▴ 170
0
votes
0
replies
527
views
I want to set the null hypothesis for the test of genetic correlation to rg=1.
correlation LDSC genetic
23 months ago by Apprentice ▴ 170
1
vote
3
replies
1.6k
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes imputation SNP
updated 11 months ago by • 0 • written 2.3 years ago by ▴ 170
1
vote
2
replies
1.1k
views
I want to identify the version of MethylationEPIC from the idat file.
Microarray methylation DNA
2.4 years ago by Apprentice ▴ 170
0
votes
1
reply
724
views
Application of repeated measurement data to missForest
R missForest
2.7 years ago by Apprentice ▴ 170
2
votes
2
replies
810
views
Significance of giving read group when using hisat2
RNA-Seq
3.1 years ago by Apprentice ▴ 170
5
votes
3
replies
1.7k
views
Unable to get all Uniprot IDs corresponding to Ensembl ID
Uniprot biomaRt
3.2 years ago by Apprentice ▴ 170
0
votes
4
replies
1.3k
views
Is it possible to infer from miRNA-seq fastq data which species it is obtained from?
miRNA-seq
3.2 years ago by Apprentice ▴ 170
4
votes
4
replies
2.4k
views
Can AlphaFold v2 predict the structure of a tetramer?
AlphaFold2
updated 3.2 years ago by ★ 2.9k • written 3.2 years ago by ▴ 170
0
votes
2
replies
958
views
How does gexpr function in ballgown package calculate the gene expression level from transcript expression levels?
ballgown FPKM R
updated 3.3 years ago by 87k • written 3.3 years ago by ▴ 170
1
vote
2
replies
1.1k
views
Can AlphaFold2 be used to predict DNA binding from fasta sequences?
DNA-binding AlphaFold2 protein
3.4 years ago by Apprentice ▴ 170
0
votes
0
replies
566
views
Applying data including both chrX variants and autosomal variants to SKAT
SKAT variant
3.4 years ago by Apprentice ▴ 170
0
votes
2
replies
2.0k
views
Imputation of X chromosome non-PAR for male subjects
SNP imputation X chromsoome
3.7 years ago by Apprentice ▴ 170
0
votes
2
replies
1.7k
views
Reference panel data to be used for GCTA-COJO
SNP GCTA
3.3 years ago by Apprentice ▴ 170
0
votes
0
replies
959
views
Preparation of a matrix of expression values of RNA-seq for input data of ssGSEA
ssGSEA RNA-seq
4.0 years ago by Apprentice ▴ 170
0
votes
0
replies
779
views
LD score regression of data including SNPs with extremely low P-value
heritability SNP LDSC
4.0 years ago by Apprentice ▴ 170
0
votes
4
replies
1.2k
views
How to draw survival curve marked at one censoring time for each patient
R survival kaplan-meier
updated 4.1 years ago by 12k • written 4.1 years ago by ▴ 170
1
vote
2
replies
1.7k
views
Annotation of pLI scores by using ANNOVAR
SNP pLI ANNOVAR
updated 4.2 years ago by ▴ 290 • written 4.2 years ago by ▴ 170
0
votes
0
replies
972
views
Can't GCTA use --bgen option for MLMA?
SNP
4.2 years ago by Apprentice ▴ 170
3
votes
4
replies
1.2k
views
Does Tophat-fusion-post need to install old blast and blast+?
RNA-Seq fusion gene
4.3 years ago by Apprentice ▴ 170
1
vote
6
replies
2.2k
views
Why does the iGenomes have decoy for only GRCh38.
RNA-Seq resequencing
written 4.3 years ago by ▴ 170
5
votes
4
replies
2.2k
views
Trimmomatic MINLEN option doesn't work
RNA-Seq
updated 4.3 years ago by 3.2k • written 4.3 years ago by ▴ 170
2
votes
2
replies
2.0k
views
URL of omictools is not available
omictools
4.5 years ago by Apprentice ▴ 170
2
votes
0
replies
845
views
Detection of excess IBD segments in patients
IBD sgements SNP
4.6 years ago by Apprentice ▴ 170
2
votes
0
replies
1.0k
views
Calculation of frequency of each haplotype from .hap file
SNP Haplotype
4.6 years ago by Apprentice ▴ 170
1
vote
2
replies
912
views
Definition of + and - strands for human genome
genome
4.8 years ago by Apprentice ▴ 170
1
vote
2
replies
1.3k
views
How to calculate covariance between betas for GxE interaction using PLINK 2.0
SNP interaction
updated 4.8 years ago by 11k • written 4.8 years ago by ▴ 170
6
votes
10
replies
5.3k
views
How to export a network of a specific module to Cytoscape - Consensus modules / multiExpr
gene expression WGCNA
updated 3.9 years ago by 89k • written 6.2 years ago by ▴ 170
4
votes
4
replies
2.9k
views
Why doesn't wgEncodeGencodeBasicV24lift37.txt.gz have annotation information of some genes?
genome gene
written 8.6 years ago by ▴ 170
6
votes
9
replies
6.9k
views
How to trim poly-sequence before or after trimming by Trimmomatic.
rna-seq
updated 5.6 years ago by 47k • written 5.6 years ago by ▴ 170
3
votes
6
replies
2.1k
views
Sex inconsistency in 1000 genomes phase 3 TSI samples
SNP
updated 5.9 years ago by 11k • written 5.9 years ago by ▴ 170
0
votes
0
replies
1.4k
views
How to convert DS value for chrX non-PAR SNPs in male
SNP imputation snp chrX PAR
6.0 years ago by Apprentice ▴ 170
1
vote
2
replies
1.1k
views
Determination of haplotypes based on genotype data of 2 SNPs
snp
6.1 years ago by Apprentice ▴ 170
62 results • Page 1 of 2
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