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seqminer:Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Maintained by Xiaowei Zhan. Last updated 6 months ago.
annotationbcfbgenmeta-analysisnext-generation-sequencingplinksequencingtabixvcfworkflowzlibbzip2libzstdsqlite3cpp
41.9 match 30 stars 8.29 score 111 scripts 6 dependentsbioc
Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.
dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp
13.9 match 28 stars 15.42 score 3.2k scripts 566 dependentsbioc
NanoMethViz:Visualise methylation data from Oxford Nanopore sequencing
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
Maintained by Shian Su. Last updated 7 days ago.
softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp
5.3 match 26 stars 6.95 score 11 scriptsbioc
methylKit:DNA methylation analysis from high-throughput bisulfite sequencing results
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
Maintained by Altuna Akalin. Last updated 16 days ago.
dnamethylationsequencingmethylseqgenome-biologymethylationstatistical-analysisvisualizationcurlbzip2xz-utilszlibcpp
3.0 match 220 stars 11.80 score 578 scripts 3 dependentspboutros
bedr:Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
Maintained by Paul C. Boutros. Last updated 6 years ago.
6.6 match 4.98 score 264 scripts 2 dependentsbioc
MungeSumstats:Standardise summary statistics from GWAS
The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.
Maintained by Alan Murphy. Last updated 3 months ago.
snpwholegenomegeneticscomparativegenomicsgenomewideassociationgenomicvariationpreprocessing
1.9 match 1 stars 5.87 score 91 scriptsbioc
biscuiteer:Convenience Functions for Biscuit
A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.
Maintained by Jacob Morrison. Last updated 5 months ago.
dataimportmethylseqdnamethylation
1.7 match 6 stars 6.16 score 16 scriptsbioc
alabaster.files:Wrappers to Save Common File Formats
Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.
Maintained by Aaron Lun. Last updated 5 months ago.
2.0 match 4.50 score 21 scripts