Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
50 results • Page
1 of 1
Sort: Views
Rank
Views
Votes
Replies
Showing top results for tag:
plink
•
reset
22
votes
4
replies
55k
views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools
plink
ped
map
updated 5.7 years ago by
hakimeazarafra
• 0 • written 10.1 years ago by
roll
▴ 350
23
votes
22
replies
54k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 23 months ago by
Nicole
• 0 • written 6.5 years ago by
gaelgarcia
▴ 270
106
votes
109
replies
52k
views
29 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 12 days ago by
LChart
4.3k • written 6.2 years ago by
Kevin Blighe
88k
5
votes
7
replies
52k
views
PLINK: merge .bed files
plink
updated 22 months ago by
Ram
44k • written 9.3 years ago by
bsmith030465
▴ 240
63
votes
16
replies
44k
views
11 follow
How To Analyze Imputed Gwas Data
gwas
r
snp
imputation
plink
updated 4.4 years ago by
Mahan
▴ 70 • written 13.6 years ago by
Stephen
2.8k
17
votes
7
replies
41k
views
6 follow
Calculating Genomic Inflation Factor
gwas
plink
updated 7.8 years ago by
GabrielMontenegro
▴ 670 • written 12.5 years ago by
Debs
▴ 30
41
votes
6
replies
33k
views
Plink: Understanding LD Clumping vs Pruning
Plink
eQTL
LD
Clumping
Pruning
updated 6.0 years ago by
Kevin Blighe
88k • written 6.0 years ago by
JourneyToAbyss
▴ 240
20
votes
15
replies
31k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 2.3 years ago by
Ram
44k • written 8.8 years ago by
dam4l
▴ 200
12
votes
25
replies
31k
views
How do I remove duplicated by position SNPs using PLink?
SNP
plink
PLINK
updated 7.0 years ago by
Kevin Blighe
88k • written 7.0 years ago by
bha
▴ 80
75
votes
60
replies
29k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 20 months ago by
Ram
44k • written 7.1 years ago by
Kevin Blighe
88k
35
votes
8
replies
28k
views
7 follow
Ibd (Identity By Descent) And The Chosen Value Of Pi_Hat
plink
updated 3.5 years ago by
Kevin Blighe
88k • written 11.4 years ago by
eXpander
▴ 170
28
votes
14
replies
23k
views
13 follow
Quick Way To Combine Two Datasets Using Only Common Markers
plink
updated 2.1 years ago by
Ram
44k • written 12.0 years ago by
pufferfish
▴ 120
7
votes
5
replies
23k
views
Keep A Subset Of Samples In Plink
plink
dataset
updated 6.6 years ago by
Ginevra
▴ 10 • written 10.8 years ago by
tom.d.brocklehurst
• 0
7
votes
9
replies
23k
views
Converting Illumina Raw Genotype Data Into Plink Ped Format
conversion
illumina
genotyping
plink
updated 8.0 years ago by
forever
▴ 80 • written 13.0 years ago by
P.NJ
▴ 50
25
votes
13
replies
23k
views
9 follow
How Does Ld In Plink Work?
plink
ld
snps
updated 10.8 years ago by
msutada
• 0 • written 11.0 years ago by
Javier2013
▴ 130
14
votes
7
replies
23k
views
Accounting for problem SNPS when merging multiple plink files
plink
snp
allele-codes
strand-flip
updated 3.1 years ago by
Ram
44k • written 10.5 years ago by
lhvkl
▴ 50
24
votes
2
replies
21k
views
Plink: Retrieving specific SNP data for individuals in dataset
plink
updated 3.0 years ago by
Ram
44k • written 10.3 years ago by
hessjl
▴ 90
9
votes
11
replies
21k
views
8 follow
Plotting Linkage Disequilibrium Decay Across The Genome
plink
ld
snps
plot
updated 3.5 years ago by
Kumar
▴ 170 • written 11.0 years ago by
Javier2013
▴ 130
11
votes
8
replies
20k
views
Remove Some Snps In Plink
plink
updated 2.7 years ago by
Ram
44k • written 12.0 years ago by
mary
▴ 210
16
votes
10
replies
20k
views
Plink filtering with physical position using a text file
plink
updated 6.5 years ago by
amcheroo
• 0 • written 7.0 years ago by
Sheila
▴ 460
12
votes
14
replies
18k
views
9 follow
Filtering Imputation output: how to filter on a VCF INFO field
imputation
filtering
minimac3
plink
vcftools
updated 6.2 years ago by
natalia.han
• 0 • written 8.2 years ago by
mmagoo6
▴ 80
19
votes
5
replies
17k
views
Converting between Impute2 and Ped/Map after imputation - 1st column dashes (--) problem
plink
imputation
updated 4.3 years ago by
Biostar
20 • written 12.7 years ago by
Philip Robinson
▴ 40
10
votes
5
replies
17k
views
Any Simple Script To Calculate Fst Value Between Populations From Genomewide Snp Data (Available In Plink Format)
snp
ped
bed
fst
plink
updated 13.4 years ago by
Davy
▴ 210 • written 13.4 years ago by
User 0422
▴ 150
16
votes
5
replies
16k
views
Convert Plink Ped Format Into Hapmap Format?
hapmap
genotyping
plink
updated 12.7 years ago by
caveman.pl
• 0 • written 12.7 years ago by
2184687-1231-83-
★ 5.1k
9
votes
11
replies
16k
views
Plink-GWAS- how to solve heterozygous haploid warning in data cleaning
Plink
genotype
SNP
updated 3.1 years ago by
Ram
44k • written 10.5 years ago by
prachimunjal14
▴ 10
8
votes
2
replies
16k
views
Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens than expected
plink
updated 7.5 years ago by
willgilks
▴ 360 • written 7.5 years ago by
msimmer92
▴ 310
13
votes
11
replies
15k
views
9 follow
plink2 bgen to vcf ukbiobank
software-error
plink
plink2
updated 18 months ago by
Ram
44k • written 5.4 years ago by
richyanicky
▴ 30
0
votes
1
reply
15k
views
Window-size in PLINK's indep-pairwise LD pruning
genome
SNP
plink
pruning
updated 6.9 years ago by
Kevin Blighe
88k • written 6.9 years ago by
solion
• 0
10
votes
4
replies
15k
views
Converting Tped To Ped
plink
ped
updated 9.0 years ago by
Simo
▴ 50 • written 11.0 years ago by
Click downvote
▴ 720
13
votes
14
replies
14k
views
How accurate is the IBD calculation by plink?
plink
IBD
8.5 years ago by
MAPK
★ 2.1k
5
votes
3
replies
14k
views
Fail to open file in plink
ped
plink
updated 5.7 years ago by
zx8754
12k • written 7.2 years ago by
janhuang.cn
▴ 230
6
votes
4
replies
14k
views
How can I convert .ped file to bed+bim+fam file using plink 1.9?
plink
SNP
next-gen
gene
ped
updated 5.6 years ago by
GenoMax
146k • written 5.6 years ago by
sofie_carolina
▴ 30
8
votes
11
replies
13k
views
11 follow
How I do lift over a Plink bim file from Hg18 to Hg19.
plink
SNP
updated 16 months ago by
jxcao9812
▴ 10 • written 7.5 years ago by
devenvyas
▴ 760
1
vote
5
replies
13k
views
Remove Duplicate Individuals From Plink Ped File Using Plink
plink
genotype
gwas
ped
updated 6.6 years ago by
Ginevra
▴ 10 • written 10.8 years ago by
venks
▴ 740
9
votes
3
replies
13k
views
PI_HAT and Z-values for relationships (PLINK IBD calculation)
plink
PI_HAT
IBD
2.4 years ago by
Ram
44k
18
votes
11
replies
13k
views
6 follow
Flip Gwas Data To Positive Strand (Hg19 Build 37)
plink
snps
gwas
updated 2.1 years ago by
Ram
44k • written 10.6 years ago by
Kevin
▴ 50
0
votes
1
reply
13k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 8.3 years ago by
Biostar
20 • written 8.3 years ago by
rednalf
▴ 90
6
votes
9
replies
12k
views
How To Extract Snps From Chromosome 1-22 In One Command From *.Bed, *.Bim And *.Fam Files
plink
snp
chromosome
updated 13.1 years ago by
Maxime Lamontagne
★ 2.4k • written 13.1 years ago by
User 0422
▴ 150
11
votes
6
replies
12k
views
6 follow
Association Analysis with Plink error
SNP
plink
plink2
association
updated 12 months ago by
rms2jg
• 0 • written 8.6 years ago by
mmukhame321
▴ 60
8
votes
4
replies
12k
views
How Can I Convert Impute2 (.Haps .Sample) To Plink (.Map .Ped)?
plink
updated 2.8 years ago by
Ram
44k • written 12.7 years ago by
Kyle Oliveira
▴ 60
9
votes
2
replies
12k
views
Convert Illumina Final Report File To Plink
illumina
plink
updated 12.8 years ago by
Maxime Lamontagne
★ 2.4k • written 12.8 years ago by
Kyle Oliveira
▴ 60
7
votes
5
replies
12k
views
Best way to convert VCF to PLINK file format and merge chromosomes?
plink
updated 2.1 years ago by
Ram
44k • written 9.1 years ago by
nchuang
▴ 260
4
votes
6
replies
12k
views
Bmerge Files In Plink
plink
updated 13.3 years ago by
biobot 0.0.77.a.1099
6.2k • written 13.3 years ago by
Zhshqzyc
▴ 520
5
votes
2
replies
12k
views
Reading Plink Files In R
plink
r
updated 7.6 years ago by
Gennady Khvorykh
▴ 100 • written 10.6 years ago by
madieke
• 0
11
votes
11
replies
12k
views
PLINK logistic regression analysis and covariates
PLINK
SNP
ASSOCIATION
3.6 years ago by
lovegenetics
▴ 70
21
votes
8
replies
11k
views
Phased Data In Plink
plink
genotyping
updated 6.0 years ago by
Shicheng Guo
★ 9.5k • written 13.5 years ago by
Pierre
▴ 500
14
votes
5
replies
11k
views
How Large Would Inbreeding Coefficient Be To Be Anomalous?
plink
updated 11.9 years ago by
jxchong
▴ 160 • written 11.9 years ago by
nnlnn
▴ 60
13
votes
11
replies
11k
views
Association Tests Using Impute2 Output
imputation
gwas
plink
updated 10.5 years ago by
Kantale
▴ 140 • written 11.2 years ago by
Khader Shameer
18k
3
votes
5
replies
11k
views
Convert 80 VCF to PED and MAP plink files
vcf
plink
format
updated 5.7 years ago by
zx8754
12k • written 8.5 years ago by
lmobuchon
▴ 40
4
votes
4
replies
11k
views
Illumina genotyping report to Plink files
SNP
conversion
Plink
Illumina
updated 2.4 years ago by
Ram
44k • written 9.6 years ago by
egustavsson
▴ 10
50 results • Page
1 of 1
Recent Votes
Comment: Finding Differential Phosphosites in TMT Phosphoproteomics Data
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
A: How do I ask a question on Biostars?
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
Recent Locations •
All
Macao,
6 minutes ago
Netherlands,
6 minutes ago
United Kingdom,
10 minutes ago
Hong Kong,
16 minutes ago
India,
22 minutes ago
United Kingdom,
35 minutes ago
Norway,
35 minutes ago
Recent Awards •
All
Popular Question
to
wangziwei0010
▴ 30
Popular Question
to
xiaoleiusc
▴ 140
Popular Question
to
odi
▴ 10
Popular Question
to
Alewa
▴ 170
Popular Question
to
Ezequiel
▴ 10
Popular Question
to
pablo
▴ 310
Popular Question
to
Jichen Wen
▴ 30
Recent Replies
Comment: Magnesium ion in a post-docking adjustment
by
dthorbur
★ 2.5k
[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type
by
conmul
• 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data
by
king
• 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation
by
Chen
• 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once?
by
GenoMax
146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset
by
allingt
• 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap
by
jared.andrews07
★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type
by
allingt
• 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis
by
allingt
• 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr
by
allingt
• 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation?
by
allingt
• 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap
by
Varun Gupta
★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA?
by
allingt
• 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is
by
i.sudbery
20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Traffic: 1492 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6