R-universe search: samtools

Showing 9 of total 9 results (show query)

blue-matter

SAMtool:Stock Assessment Methods Toolkit

Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.

Maintained by Quang Huynh. Last updated 21 days ago.

cpp

61.1 match 3 stars 6.49 score 36 scripts 1 dependents

bioc

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.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

4.2 match 28 stars 15.42 score 3.2k scripts 566 dependents

bioc

epialleleR:Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

Maintained by Oleksii Nikolaienko. Last updated 13 days ago.

dnamethylation epigenetics methylseq longread bioconductor dna-methylation epiallele next-generation-sequencing samtools curl bzip2 xz-utils zlib cpp

10.0 match 4 stars 5.94 score 5 scripts

bioc

scPipe:Pipeline for single cell multi-omic data pre-processing

A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.

Maintained by Shian Su. Last updated 3 months ago.

immunooncology software sequencing rnaseq geneexpression singlecell visualization sequencematching preprocessing qualitycontrol genomeannotation dataimport curl bzip2 xz-utils zlib cpp

1.8 match 68 stars 9.02 score 84 scripts

wanglabcsu

blit:Bioinformatics Library for Integrated Tools

An all-encompassing R toolkit designed to streamline the process of calling various bioinformatics software and then performing data analysis and visualization in R. With 'blit', users can easily integrate a wide array of bioinformatics command line tools into their workflows, leveraging the power of R for sophisticated data manipulation and graphical representation.

Maintained by Yun Peng. Last updated 3 days ago.

3.0 match 3 stars 4.38 score 3 scripts

blue-matter

openMSE:Easily Install and Load the 'openMSE' Packages

The 'openMSE' package is designed for building operating models, doing simulation modelling and management strategy evaluation for fisheries. 'openMSE' is an umbrella package for the 'MSEtool' (Management Strategy Evaluation toolkit), 'DLMtool' (Data-Limited Methods toolkit), and SAMtool (Stock Assessment Methods toolkit) packages. By loading and installing 'openMSE', users have access to the full functionality contained within these packages. Learn more about 'openMSE' at <https://openmse.com/>.

Maintained by Adrian Hordyk. Last updated 6 months ago.

2.2 match 14 stars 5.57 score 89 scripts

bioc

Rbowtie2:An R Wrapper for Bowtie2 and AdapterRemoval

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

Maintained by Zheng Wei. Last updated 2 months ago.

sequencing alignment preprocessing cpp

1.9 match 5.51 score 24 scripts 3 dependents

cran

varitas:Variant Calling in Targeted Analysis Sequencing Data

Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.

Maintained by Adam Mills. Last updated 4 years ago.

1.1 match 2.30 score

bioc

appreci8R:appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.

Maintained by Sarah Sandmann. Last updated 5 months ago.

variantdetection geneticvariability snp variantannotation sequencing

0.5 match 3.30 score 1 scripts