Paket: pigx-rnaseq (0.1.0-1.1)

[ Quellcode: 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.

Andere Pakete mit Bezug zu 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

  oder rna-star

  ultrafast universal RNA-seq aligner

• dep: libjs-jquery-datatables

  jQuery-Plug-in, das aus verschiedenen Datenquellen schöne Tabellen erstellt

• dep: libjs-jquery-tablesorter

  jQuery-Plungin für flexible clientseitige Sortierung von Tabellen

• 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 - Interaktivität zwischen HTML-Widgets

• dep: r-cran-data.table

  GNU R - Erweiterung von data.frame()

• dep: r-cran-dt (>= 0.15+dfsg-2)

  GNU R wrapper of the JavaScript library 'DataTables'

• dep: r-cran-ggplot2

  Implementierung der »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

  Konvertierung von R-Markdown-Dokumenten in verschiedene Formate

• dep: r-cran-scales

  Skalierungsfunktionen zur Visualisierung

• 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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