套件：trinityrnaseq（2.15.1+dfsg-2） [debports]
RNA-Seq De novo Assembly
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.
其他與 trinityrnaseq 有關的套件
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- dep: berkeley-express
- Streaming quantification for high-throughput sequencing
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- dep: bowtie
- Ultrafast memory-efficient short read aligner
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- dep: bowtie2
- ultrafast memory-efficient short read aligner
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- dep: default-jre-headless
- Standard Java or Java compatible Runtime (headless)
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- dep: jaligner
- Smith-Waterman algorithm with Gotoh's improvement
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- dep: jellyfish
- count k-mers in DNA sequences
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- dep: kallisto
- near-optimal RNA-Seq quantification
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- dep: libc6.1 (>= 2.34)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6.1-udeb
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- dep: libgcc-s1 (>= 3.4)
- GCC 支援函式庫
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- dep: libgetopt-java
- GNU getopt - Java port
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- dep: libgomp1 (>= 6)
- GCC OpenMP (GOMP) support library
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- dep: libhts3 (>= 1.17)
- C library for high-throughput sequencing data formats
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- dep: libjung-free-java
- Java Universal Network/Graph Framework
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- dep: libstdc++6 (>= 13.1)
- GNU Standard C++ Library v3
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- dep: liburi-perl
- module to manipulate and access URI strings
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- dep: libwww-perl
- simple and consistent interface to the world-wide web
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- dep: ncbi-blast+
- next generation suite of BLAST sequence search tools
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- dep: parafly
- parallel command processing using OpenMP
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- dep: perl
- Larry Wall's Practical Extraction and Report Language
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-htseq
- Python3 high-throughput genome sequencing read analysis utilities
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- dep: r-base-core
- GNU R core of statistical computation and graphics system
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- dep: rsem
- RNA-Seq by Expectation-Maximization
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- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- dep: subread
- toolkit for processing next-gen sequencing data
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- dep: trimmomatic
- flexible read trimming tool for Illumina NGS data
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- dep: zlib1g (>= 1:1.1.4)
- 壓縮函式庫 - 跑程式時用(runtime)
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- rec: curl
- command line tool for transferring data with URL syntax
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- rec: gmap
- spliced and SNP-tolerant alignment for mRNA and short reads
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- rec: hisat2
- graph-based alignment of short nucleotide reads to many genomes
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- rec: picard-tools
- Command line tools to manipulate SAM and BAM files
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- rec: python3-hisat2
- Python scripts accompanying hisat2
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- rec: python3-numpy
- Fast array facility to the Python language (Python 3)
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- rec: r-bioc-biobase
- base functions for Bioconductor
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- rec: r-bioc-ctc
- Cluster and Tree Conversion
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- rec: r-bioc-deseq2
- R package for RNA-Seq Differential Expression Analysis
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- rec: r-bioc-dexseq
- GNU R inference of differential exon usage in RNA-Seq
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- rec: r-bioc-edger
- Empirical analysis of digital gene expression data in R
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- rec: r-bioc-goseq
- GNU R gene ontology analyser for RNA-seq and other length biased data
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- rec: r-bioc-qvalue
- GNU R package for Q-value estimation for FDR control
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- rec: r-bioc-rots
- GNU R Teproducibility-Optimized Test Statistic
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- rec: r-cran-ape
- GNU R package for Analyses of Phylogenetics and Evolution
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- rec: r-cran-argparse
- GNU R command line parser for optional and positional arguments
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- rec: r-cran-cluster
- GNU R package for cluster analysis by Rousseeuw et al
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- rec: r-cran-fastcluster
- Fast hierarchical clustering routines for GNU R
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- rec: r-cran-goplot
- GNU R visualization of functional analysis data
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- rec: r-cran-gplots
- GNU R package with tools for plotting data by Greg Warnes et al
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- rec: r-cran-kernsmooth
- GNU R package for kernel smoothing and density estimation
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- rec: r-cran-readr
- GNU R package to read rectangular text data
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- rec: r-cran-tidyverse
- Easily Install and Load the 'Tidyverse'
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- rec: rna-star
- ultrafast universal RNA-seq aligner
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- rec: salmon
- wicked-fast transcript quantification from RNA-seq data
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- rec: tabix
- generic indexer for TAB-delimited genome position files
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- rec: trinityrnaseq-examples
- RNA-Seq De novo Assembly common example and testing files
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- sug: collectl
- Utility to collect Linux performance data
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- sug: r-bioc-tximport
- transcript-level estimates for biological sequencing
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- sug: r-bioc-tximportdata
- GNU R various transcript abundance quantifiers
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- sug: transdecoder
- find coding regions within RNA transcript sequences