[ 原始碼： pigx-rnaseq ]
套件：pigx-rnaseq（0.1.0-1.1）
pipeline for checkpointed and distributed RNA-seq analyses
This package provides a automated workflow for the automated analysis of RNA-seq experiments. A series of well-accecpted tools are connected in Python scripts and controlled via snakemake. This supports the parallel execution of these workflows and provides checkpointing, such that interrupted workflows can take up their work again.
其他與 pigx-rnaseq 有關的套件
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- dep: fastp
- Ultra-fast all-in-one FASTQ preprocessor
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- dep: fastqc
- quality control for high throughput sequence data
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- dep: libjs-jquery-datatables
- jQuery plug-in that makes nice tables from different data sources
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- dep: libjs-jquery-tablesorter
- jQuery flexible client-side table sorting plugin
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- dep: megadepth
- computes coverage from BigWig and BAM sequencing files
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- dep: multiqc
- output integration for RNA sequencing across tools and samples
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-deeptools
- platform for exploring biological deep-sequencing data
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- dep: python3-htseq
- Python3 high-throughput genome sequencing read analysis utilities
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- dep: r-bioc-deseq2
- R package for RNA-Seq Differential Expression Analysis
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- dep: r-bioc-rtracklayer
- GNU R interface to genome browsers and their annotation tracks
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- dep: r-bioc-summarizedexperiment
- BioConductor assay container
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- dep: r-bioc-tximport
- transcript-level estimates for biological sequencing
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- dep: r-cran-corrplot
- Visualization of a Correlation Matrix
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- dep: r-cran-crosstalk
- GNU R inter-widget interactivity for HTML widgets
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- dep: r-cran-data.table
- GNU R extension of Data.frame
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- dep: r-cran-dt (>= 0.15+dfsg-2)
- GNU R wrapper of the JavaScript library 'DataTables'
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- dep: r-cran-ggplot2
- implementation of the Grammar of Graphics
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- dep: r-cran-ggpubr
- GNU R ggplot2 based publication ready plots
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- dep: r-cran-ggrepel
- auto-position non-overlapping text labels in plots
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- dep: r-cran-gprofiler2
- Interface to the 'g:Profiler' Toolset
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- dep: r-cran-pheatmap
- GNU R package to create pretty heatmaps
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- dep: r-cran-plotly
- create interactive web graphics via 'plotly.js' in GNU R
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- dep: r-cran-reshape2
- Flexibly reshape data: a reboot of the reshape package
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- dep: r-cran-rjson
- GNU R package for converting between R and JSON objects
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- dep: r-cran-rlang
- Functions for Base Types and Core R and 'Tidyverse' Features
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- dep: r-cran-rmarkdown
- convert R markdown documents into a variety of formats
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- dep: r-cran-scales
- Scale functions for visualization
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- dep: salmon
- wicked-fast transcript quantification from RNA-seq data
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- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- dep: snakemake
- pythonic workflow management system
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- dep: trim-galore
- automate quality and adapter trimming for DNA sequencing