Пакунок: pigx-rnaseq (0.1.1-1)

[ Source: pigx-rnaseq  ]

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.

Інші пакунки пов'язані з pigx-rnaseq

• dep: fastp

  Ultra-fast all-in-one FASTQ preprocessor

• dep: fastqc

  quality control for high throughput sequence data

• dep: hisat2

  graph-based alignment of short nucleotide reads to many genomes

  or rna-star

  ultrafast universal RNA-seq aligner

• dep: libjs-jquery-datatables

  jQuery plug-in that makes nice tables from different data sources

• dep: libjs-jquery-tablesorter

  jQuery flexible client-side table sorting plugin

• dep: megadepth

  computes coverage from BigWig and BAM sequencing files

• dep: multiqc

  output integration for RNA sequencing across tools and samples

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-deeptools

  platform for exploring biological deep-sequencing data

• dep: python3-htseq

  Python3 high-throughput genome sequencing read analysis utilities

• dep: r-bioc-deseq2

  R package for RNA-Seq Differential Expression Analysis

• dep: r-bioc-rtracklayer

  GNU R interface to genome browsers and their annotation tracks

• dep: r-bioc-summarizedexperiment

  BioConductor assay container

• dep: r-bioc-tximport

  transcript-level estimates for biological sequencing

• dep: r-cran-corrplot

  Visualization of a Correlation Matrix

• dep: r-cran-crosstalk

  GNU R inter-widget interactivity for HTML widgets

• dep: r-cran-data.table

  GNU R extension of Data.frame

• dep: r-cran-dt

  GNU R wrapper of the JavaScript library 'DataTables'

• dep: r-cran-ggplot2

  implementation of the Grammar of Graphics

• dep: r-cran-ggpubr

  GNU R ggplot2 based publication ready plots

• dep: r-cran-ggrepel

  auto-position non-overlapping text labels in plots

• dep: r-cran-gprofiler2

  Interface to the 'g:Profiler' Toolset

• dep: r-cran-pheatmap

  GNU R package to create pretty heatmaps

• dep: r-cran-plotly

  create interactive web graphics via 'plotly.js' in GNU R

• dep: r-cran-reshape2

  Flexibly reshape data: a reboot of the reshape package

• dep: r-cran-rjson

  GNU R package for converting between R and JSON objects

• dep: r-cran-rlang

  Functions for Base Types and Core R and 'Tidyverse' Features

• dep: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• dep: r-cran-scales

  Scale functions for visualization

• dep: salmon

  wicked-fast transcript quantification from RNA-seq data

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: snakemake

  pythonic workflow management system

• dep: trim-galore

  automate quality and adapter trimming for DNA sequencing

• rec: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• rec: rna-star

  ultrafast universal RNA-seq aligner

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