[ 源代码： trinityrnaseq ]
软件包：trinityrnaseq（2.11.0+dfsg-6）
trinityrnaseq 的相关链接
Debian 的资源：
下载源码包 trinityrnaseq：
- [trinityrnaseq_2.11.0+dfsg-6.dsc]
- [trinityrnaseq_2.11.0+dfsg.orig.tar.xz]
- [trinityrnaseq_2.11.0+dfsg-6.debian.tar.xz]
维护小组：
外部的资源：
- 主页 [trinityrnaseq.github.io]
相似软件包：
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.
其他与 trinityrnaseq 有关的软件包
|
|
|
|
-
- dep: berkeley-express
- Streaming quantification for high-throughput sequencing
-
- dep: bowtie
- Ultrafast memory-efficient short read aligner
-
- dep: bowtie2
- ultrafast memory-efficient short read aligner
-
- dep: curl
- command line tool for transferring data with URL syntax
-
- dep: default-jre-headless
- Standard Java or Java compatible Runtime (headless)
-
- dep: gmap
- spliced and SNP-tolerant alignment for mRNA and short reads
-
- dep: hisat2
- graph-based alignment of short nucleotide reads to many genomes
-
- dep: jaligner
- Smith-Waterman algorithm with Gotoh's improvement
-
- dep: jellyfish
- count k-mers in DNA sequences
-
- dep: kallisto
- near-optimal RNA-Seq quantification
-
- dep: libc6 (>= 2.27)
- GNU C 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6-udeb
-
- dep: libcommons-collections4-java
- Apache Commons Collections - Extended Collections API for Java
-
- dep: libgcc-s1 (>= 3.0)
- GCC 支持库
-
- dep: libgetopt-java
- GNU getopt - Java port
-
- dep: libgomp1 (>= 6)
- GCC OpenMP（GOMP）支持库
-
- dep: libhts3 (>= 1.10)
- C library for high-throughput sequencing data formats
-
- dep: libjung-free-java
- Java Universal Network/Graph Framework
-
- dep: libstdc++6 (>= 9)
- GNU 标准 C++ 库，第3版
-
- dep: liburi-perl
- module to manipulate and access URI strings
-
- dep: libwww-perl
- simple and consistent interface to the world-wide web
-
- dep: ncbi-blast+
- next generation suite of BLAST sequence search tools
-
- dep: parafly
- parallel command processing using OpenMP
-
- dep: perl
- 拉里 沃尔的实用报表提取语言(Perl)
-
- dep: python3
- 交互式高级面向对象语言（默认 python3 版本）
-
- dep: python3-hisat2
- Python scripts accompanying hisat2
-
- dep: python3-htseq
- Python3 high-throughput genome sequencing read analysis utilities
-
- dep: python3-numpy
- Fast array facility to the Python 3 language
-
- dep: r-base-core
- GNU R core of statistical computation and graphics system
-
- dep: r-bioc-biobase
- base functions for Bioconductor
-
- dep: r-bioc-ctc
- Cluster and Tree Conversion
-
- dep: r-bioc-deseq2
- R package for RNA-Seq Differential Expression Analysis
-
- dep: r-bioc-dexseq
- GNU R inference of differential exon usage in RNA-Seq
-
- dep: r-bioc-edger
- Empirical analysis of digital gene expression data in R
-
- dep: r-bioc-goseq
- GNU R gene ontology analyser for RNA-seq and other length biased data
-
- dep: r-bioc-qvalue
- GNU R package for Q-value estimation for FDR control
-
- dep: r-bioc-rots
- GNU R Teproducibility-Optimized Test Statistic
-
- dep: r-bioc-tximport
- transcript-level estimates for biological sequencing
-
- dep: r-cran-ape
- GNU R package for Analyses of Phylogenetics and Evolution
-
- dep: r-cran-argparse
- GNU R command line parser for optional and positional arguments
-
- dep: r-cran-cluster
- GNU R package for cluster analysis by Rousseeuw et al
-
- dep: r-cran-fastcluster
- Fast hierarchical clustering routines for GNU R
-
- dep: r-cran-goplot
- GNU R visualization of functional analysis data
-
- dep: r-cran-gplots
- GNU R package with tools for plotting data by Greg Warnes et al
-
- dep: r-cran-readr
- GNU R package to read rectangular text data
-
- dep: rna-star
- ultrafast universal RNA-seq aligner
-
- dep: rsem
- RNA-Seq by Expectation-Maximization
-
- dep: salmon
- wicked-fast transcript quantification from RNA-seq data
-
- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
-
- dep: subread
- toolkit for processing next-gen sequencing data
-
- dep: transdecoder
- find coding regions within RNA transcript sequences
-
- dep: trimmomatic
- flexible read trimming tool for Illumina NGS data
-
- dep: zlib1g (>= 1:1.1.4)
- 压缩库 - 运行时
-
- rec: picard-tools
- Command line tools to manipulate SAM and BAM files
-
- rec: r-cran-tidyverse
- Easily Install and Load the 'Tidyverse'
-
- rec: tabix
- generic indexer for TAB-delimited genome position files
-
- rec: trinityrnaseq-examples
- RNA-Seq De novo Assembly common example and testing files
-
- sug: collectl
- Utility to collect Linux performance data
-
- sug: r-bioc-tximportdata
- 软件包暂时不可用