Package: SeqSQC 1.29.0

Qian Liu

SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

Authors:Qian Liu [aut, cre]

SeqSQC_1.29.0.tar.gz
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SeqSQC.pdf |SeqSQC.html✨
SeqSQC/json (API)
NEWS

# Install 'SeqSQC' in R:

install.packages('SeqSQC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/liubuntu/seqsqc/issues

On BioConductor:SeqSQC-1.29.0(bioc 3.21)SeqSQC-1.28.0(bioc 3.20)

experiment data homo_sapiens_data sequencing data project1000genomes genome

5.38 score 2 scripts 398 downloads 2 mentions 17 exports 112 dependencies

Last updated 2 months agofrom:42fdfb6802. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-win	WARNING	Nov 25 2024
R-4.5-linux	WARNING	Nov 25 2024
R-4.4-win	WARNING	Nov 25 2024
R-4.4-mac	WARNING	Nov 25 2024
R-4.3-win	WARNING	Nov 25 2024
R-4.3-mac	WARNING	Nov 25 2024

Exports:gdsfile gdsfile<-IBDCheck IBDRemove Inbreeding LoadVfile MissingRate PCACheck plotQC problemList QCresult QCresult<-RenderReport sampleQC SeqOpen SeqSQC SexCheck

Dependencies:AnnotationDbi AnnotationHub askpass base64enc Biobase BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob bslib cachem class cli colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr digest dplyr e1071 evaluate ExperimentHub fansi farver fastmap filelock fontawesome forcats fs gdsfmt generics GenomeInfoDb GenomeInfoDbData GenomicRanges GGally ggplot2 ggstats glue gtable highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr plotly plyr png prettyunits progress promises proxy purrr R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown RSQLite S4Vectors sass scales SNPRelate stringi stringr sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

Sample Quality Check for NGS Data using SeqSQC package

Qian Liu, Qianqian Zhu

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2018-08-30
Started: 2017-08-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sample Quality Check for NGS Data using SeqSQC package	SeqSQC-package
Example capture region file used in vignette.	CCDS.Hs37.3.reduced_chr1.bed
Example vcf file used in vignette.	example_sub.vcf
example gds file used in vignette.	example.gds
Example SeqSQC file used in vignette.	example.seqfile.Rdata
Sample relationship check with SeqSQC object input file.	IBDCheck
Obtain the problematic sample list from IBD relatedness.	IBDRemove
Sample inbreeding check with SeqSQC object input file.	Inbreeding
Data preprocessing for VCF or plink input from NGS or GWAS data.	LoadVfile
Sample missing rate check with SeqSQC object input file.	MissingRate
Population outlier check with SeqSQC object input file.	PCACheck
Plot the QC results for specific QC steps.	plotQC
Generate the problematic sample list.	problemList
Render the rmarkdown file for generating a sample QC report.	RenderReport
Sample annotation file for the example data used in vignette.	sampleAnnotation.txt
The wrap-up function for sample QC of sequencing/GWAS data.	sampleQC
Open the gds file in SeqSQC objects.	SeqOpen
A data format to store genotype phenotype and sample QC results from SeqSQC.	"gdsfile<-",SeqSQC-method "QCresult<-",SeqSQC-method gdsfile gdsfile,SeqSQC-method gdsfile<- gdsfile<-,SeqSQC-method QCresult QCresult,SeqSQC-method QCresult<- QCresult<-,SeqSQC-method SeqSQC SeqSQC-class
Sample gender check with SeqSQC object input file.	SexCheck