2024-03-28T09:45:33Z
https://zenodo.org/oai2d
oai:zenodo.org:1239670
2020-01-21T07:23:03Z
user-macrophage-tuqtls
openaire_data
Alasoo, Kaur
2018-05-02
<p>Column names:</p>
<ol>
<li>phenotype_id</li>
<li>pheno_chr</li>
<li>pheno_start</li>
<li>pheno_end</li>
<li>strand - strand of the phenotype</li>
<li>n_snps - number of SNPs tested per phenotype</li>
<li>distance - distance from the variant to the phenotype</li>
<li>snp_id</li>
<li>snp_chr</li>
<li>snp_start - position of the SNP</li>
<li>snp_end - same as snp_start</li>
<li>p_nominal - nominal p-value from QTLTools</li>
<li>beta - effect size from QTLTools</li>
<li>is_lead - is the variant the lead QTL for the phenotype?</li>
</ol>
https://doi.org/10.5281/zenodo.1239670
oai:zenodo.org:1239670
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.1239669
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Summary statistics of transcript usage QTLs in naive and stimulated macrophages (part 1)
info:eu-repo/semantics/other
oai:zenodo.org:1245778
2020-01-20T16:25:54Z
user-macrophage-tuqtls
Alasoo, Kaur
2018-05-11
<p>These are the standard QTLtools (https://qtltools.github.io/qtltools/) output files with the following column names:</p>
<ol>
<li>The phenotype <strong>group</strong> ID (here a gene ID)</li>
<li>The chromosome ID of the phenotype group</li>
<li>The start position of the phenotype group</li>
<li>The end position of the phenotype group</li>
<li>The strand orientation of the phenotype group</li>
<li><strong>The top phenotype in the group</strong> (here an exon ID)</li>
<li><strong>The total number of phenotypes in the group</strong> (i.e. #exons)</li>
<li>The total number of variants tested in <em>cis</em></li>
<li>The distance between the phenotype group and the tested variant (accounting for strand orientation)</li>
<li>The ID of the top variant</li>
<li>The chromosome ID of the top variant</li>
<li>The start position of the top variant</li>
<li>The end position of the top variant</li>
<li>The number of degrees of freedom used to compute the P-values</li>
<li>Dummy</li>
<li>The first parameter value of the fitted beta distribution</li>
<li>The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region)</li>
<li>The nominal P-value of association between the top phenotype and the top variant in <em>cis</em></li>
<li>The corresponding regression slope</li>
<li>The P-value of association adjusted for the number of variants and phenotypes tested in <em>cis</em> given by the direct method (i.e. empirircal P-value)</li>
<li>The P-value of association adjusted for the number of variants and phenotypes tested in <em>cis</em> given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis</li>
</ol>
<p>I prefer to use the following short column names</p>
<ol>
<li>group_id</li>
<li>pheno_chr</li>
<li>pheno_start</li>
<li>pheno_end</li>
<li>strand</li>
<li>phenotype_id</li>
<li>group_size</li>
<li>n_cis_snps</li>
<li>distance</li>
<li>snp_id</li>
<li>snp_chr</li>
<li>snp_start</li>
<li>snp_end</li>
<li>df</li>
<li>dummy</li>
<li>beta1</li>
<li>beta2</li>
<li>p_nominal</li>
<li>slope</li>
<li>p_perm</li>
<li>p_beta</li>
</ol>
<p> </p>
https://doi.org/10.5281/zenodo.1245778
oai:zenodo.org:1245778
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.1245777
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
QTL lead variants
info:eu-repo/semantics/article
oai:zenodo.org:1245513
2020-01-24T19:21:56Z
user-macrophage-tuqtls
openaire_data
Alasoo, Kaur
2018-05-11
<p>Column names:</p>
<ol>
<li>phenotype_id</li>
<li>pheno_chr</li>
<li>pheno_start</li>
<li>pheno_end</li>
<li>strand - strand of the phenotype</li>
<li>n_snps - number of SNPs tested per phenotype</li>
<li>distance - distance from the variant to the phenotype</li>
<li>snp_id</li>
<li>snp_chr</li>
<li>snp_start - position of the SNP</li>
<li>snp_end - same as snp_start</li>
<li>p_nominal - nominal p-value from QTLTools</li>
<li>beta - effect size from QTLTools</li>
<li>is_lead - is the variant the lead QTL for the phenotype?</li>
</ol>
https://doi.org/10.5281/zenodo.1245513
oai:zenodo.org:1245513
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.1245512
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Summary statistics of transcript usage QTLs in naive and stimulated macrophages (part 2)
info:eu-repo/semantics/other
oai:zenodo.org:1245544
2020-01-24T19:23:38Z
user-macrophage-tuqtls
openaire_data
Alasoo, Kaur
2018-05-11
<p>Colocalisation between QTLs and summary statistics from complex traits</p>
https://doi.org/10.5281/zenodo.1245544
oai:zenodo.org:1245544
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.1245543
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Colocalisation between QTLs and summary statistics from complex traits
info:eu-repo/semantics/other
oai:zenodo.org:1245602
2020-01-24T19:21:59Z
user-macrophage-tuqtls
openaire_data
Alasoo, Kaur
2018-05-11
<p>Column names</p>
<ol>
<li>chr - chromosome name</li>
<li>pos - position</li>
<li>snp_id - variant id</li>
<li>ref - reference allele</li>
<li>alt - alternate allele</li>
<li>type - variant type (SNP or INDEL)</li>
<li>AC - alternate allele count</li>
<li>AN - total allele count</li>
</ol>
https://doi.org/10.5281/zenodo.1245602
oai:zenodo.org:1245602
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.1245601
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Coordinates of genetic variants used for QTL mapping
info:eu-repo/semantics/other
oai:zenodo.org:1245133
2020-01-24T19:23:13Z
user-macrophage-tuqtls
openaire_data
Alasoo, Kaur
2018-05-10
<p>Differential gene expression results from DESeq2</p>
https://doi.org/10.5281/zenodo.1245133
oai:zenodo.org:1245133
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.1245132
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Differential gene expression results from DESeq2
info:eu-repo/semantics/other
oai:zenodo.org:2571453
2020-01-24T19:25:45Z
user-macrophage-tuqtls
openaire_data
Alasoo, Kaur
2019-02-18
<p>Raw and normalised read count matrices together with metadata.</p>
https://doi.org/10.5281/zenodo.2571453
oai:zenodo.org:2571453
Zenodo
https://zenodo.org/communities/macrophage-tuqtls
https://doi.org/10.5281/zenodo.2571452
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Processed gene expression read counts from the AcLDL and IFNg+Salmonella studies
info:eu-repo/semantics/other