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19 results • Page
1 of 1
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Views
Votes
Replies
3
votes
4
replies
4.8k
views
How to visualize sequence quality control distribution
sequence
Fastq
R
updated 15 hours ago by
Ram
38k • written 7.4 years ago by
faizlotfy
▴ 30
0
votes
0
replies
1.0k
views
Getting started with miRNA prediction
miRNA
updated 19 hours ago by
Ram
38k • written 7.4 years ago by
Nuria_bl
▴ 10
0
votes
3
replies
821
views
Problem to convert genotypes to plink format from bcftools
vcf
bcftools
ped
plink
beagle
updated 23 hours ago by
Manuel Ramón
▴ 10 • written 22 months ago by
Alejandro
▴ 10
1
vote
4
replies
367
views
SKAT in R
pvalue
skat
snp
52 minutes ago by
Eliza
▴ 20
1
vote
4
replies
311
views
Snakemake doesn't recognize output files even though they are created
python
Snakemake
12 hours ago by
DdogBoss
• 0
0
votes
2
replies
288
views
LDSC correlation calculate confidence intervals
correlation
intervals
confidence
genetic
LDSC
13 hours ago by
YL
▴ 10
0
votes
3
replies
182
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
7 hours ago by
dare_devil
★ 1.7k
0
votes
1
reply
155
views
Difference between sratools and sratoolkit
sratools
fastq
sequencing
sratoolkit
sra
updated 22 hours ago by
GenoMax
127k • written 1 day ago by
hamarillo
▴ 10
0
votes
1
reply
138
views
R package for functional enrichment and depletion analysis
enrichment
depletion
updated 15 hours ago by
rpolicastro
11k • written 18 hours ago by
lessismore
★ 1.3k
0
votes
1
reply
126
views
KEGG analysis in Hordeum
KEGG
vulgare
miRNA
transcripts
Hordeum
updated 19 hours ago by
GenoMax
127k • written 22 hours ago by
martta95
• 0
1
vote
1
reply
116
views
My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
R
ENSEMBL
DESeq2
updated 11 hours ago by
GenoMax
127k • written 12 hours ago by
rgomez
• 0
0
votes
1
reply
114
views
Plink-association test
association
plink
case-control
covar
updated 23 hours ago by
Nicolas Rosewick
10k • written 1 day ago by
Viktor Messi
• 0
0
votes
1
reply
108
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 1 hour ago by
pinheirofabiano
▴ 10 • written 17 hours ago by
reventropy2003
• 0
0
votes
1
reply
107
views
""ERROR:States for individual 0 are zero " when I using GLIMPSE2 for Imputation
PBWT
imputation
gene
GLIMPSE2
updated 20 hours ago by
4galaxy77
2.6k • written 23 hours ago by
2013677172
• 0
0
votes
1
reply
98
views
Gene family classification using RNA-seq data
RNA_seq
gene_expression
gene_family
updated 19 hours ago by
jv
★ 1.0k • written 20 hours ago by
Dion
• 0
0
votes
0
replies
90
views
HiC analysis in R
R
HiC
updated 15 hours ago by
Ram
38k • written 16 hours ago by
gitprohub4
• 0
0
votes
0
replies
73
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
SAM
BAM
Fields
bamCoverage
deeptools
12 hours ago by
Deep
• 0
0
votes
0
replies
72
views
Seraut JackStrawplot PC1
jackstrawplot
Seurat
scRNAseq
PCA
updated 20 hours ago by
Ram
38k • written 22 hours ago by
miyeok
• 0
0
votes
0
replies
7
views
How to find p-values for annotated methylated regions using methylkit and genomation
NGS
bioinformatics
pvalue
annotation
methylationarray
19 minutes ago by
Saransh
• 0
19 results • Page
1 of 1
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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zhou_1228
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GenoMax
127k
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Mensur Dlakic
★ 23k
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Recent Replies
Comment: SKAT in R
by
Eliza
▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
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