软件包：berkeley-express（1.5.2+dfsg-1 以及其他的）
berkeley-express 的相关链接
Debian 的资源：
下载源码包 berkeley-express：
- [berkeley-express_1.5.2+dfsg-1.dsc]
- [berkeley-express_1.5.2+dfsg.orig.tar.xz]
- [berkeley-express_1.5.2+dfsg-1.debian.tar.xz]
维护小组：
外部的资源：
- 主页 [bio.math.berkeley.edu]
相似软件包：
Streaming quantification for high-throughput sequencing
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk.
In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias.
eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance.
其他与 berkeley-express 有关的软件包
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- dep: libbamtools2.5.1
- dynamic library for manipulating BAM (genome alignment) files
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- dep: libboost-atomic1.67.0
- atomic data types, operations, and memory ordering constraints
-
- dep: libboost-chrono1.67.0
- C++ representation of time duration, time point, and clocks
-
- dep: libboost-date-time1.67.0
- set of date-time libraries based on generic programming concepts
-
- dep: libboost-filesystem1.67.0
- filesystem operations (portable paths, iteration over directories, etc) in C++
-
- dep: libboost-program-options1.67.0
- program options library for C++
-
- dep: libboost-system1.67.0
- Operating system (e.g. diagnostics support) library
-
- dep: libboost-thread1.67.0
- portable C++ multi-threading
-
- 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
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- dep: libgcc1 (>= 1:3.0) [amd64]
- GCC 支持库
- dep: libgcc1 (>= 1:3.5) [armhf]
- dep: libgcc1 (>= 1:4.2) [i386]
- dep: libgcc1 (>= 1:4.5) [arm64]
-
- dep: libprotobuf17
- protocol buffers C++ library
-
- dep: libstdc++6 (>= 5.2)
- GNU 标准 C++ 库，第3版
-
- rec: med-config (>= 2.1)
- Debian Med general config package