Available Tools
ShennongTools provides 19 pre-configured bioinformatics tools:
| Tool | Description | Commands |
|---|---|---|
| Bedtools | A powerful toolset for genome arithmetic. | intersect, merge, sort, genomecov |
| Deeptools | A suite of tools to process and visualize deep sequencing data | bamcoverage, computematrix, plotheatmap, plotpr… |
| Fastp | Fast all-in-one preprocessing for FastQ files | trim |
| Fastqc | Quality control tool for high throughput sequence data | run |
| Hisat2 | Fast and sensitive alignment of sequencing reads to a population of genomes | index, align |
| Kallisto | Quantification of transcript abundances from RNA-Seq data | index, quant |
| Kraken2 | Kraken 2 is a taxonomic classification system for metagenomics | classify, build |
| Macs2 | Model-based Analysis of ChIP-Seq (MACS2) for peak calling | callpeak, bdgcmp |
| Multiqc | Aggregate results from bioinformatics analyses into a single report | run |
| Pyscenic | pySCENIC is a python implementation of the SCENIC pipeline to infer gene regulatory networks from single-cell RNA-seq data. | grn, ctx, aucell |
| Salmon | A tool for transcript-level quantification from RNA-seq data using quasi-mapping | index, quant |
| Sambamba | Fast and efficient BAM file processing tool written in D | view, sort, index, markdup, flagstat |
| Samtools | Utilities for manipulating alignments in the SAM, BAM, and CRAM formats | view, index, sort, faidx, fastq |
| Scanpy | Scanpy: scalable toolkit for analyzing single-cell gene expression data | normalize, filter_cells, filter_genes, find_hvg… |
| Seqkit | A cross-platform and ultrafast toolkit for FASTA/Q file manipulation | seq, stats, grep, fx2tab, rmdup |
| Sra Tools | Toolkit for accessing and converting SRA data | prefetch, fasterq_dump |
| Star | Spliced Transcripts Alignment to a Reference (STAR) | index, align, solo |
| Stringtie | Transcript assembly and quantification for RNA-Seq | quant, merge |
| Subread | A ultrafast and accurate read summarization program | featurecounts, buildindex |
Quick Start
library(ShennongTools)
# List all available tools
sn_list_tools()
# Get help for a specific tool
sn_help("samtools")
# Run a tool command
result <- sn_run("samtools", "view",
input = "alignment.bam",
output = "filtered.bam",
flags = "-q 30"
)