パッケージ: rsem (1.3.3+dfsg-1)
RNA-Seq by Expectation-Maximization
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute’s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.
その他の rsem 関連パッケージ
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- dep: libc6 (>= 2.15)
- GNU C ライブラリ: 共有ライブラリ
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: libgcc-s1 (>= 3.0)
- GCC 共有ライブラリ
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- dep: libhts3 (>= 1.10)
- C library for high-throughput sequencing data formats
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- dep: libstdc++6 (>= 9)
- GNU 標準 C++ ライブラリ v3
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- dep: perl
- Larry Wall 作の実用的な抽出とレポート用の言語
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- dep: python3
- 対話式の高レベルオブジェクト指向言語 (デフォルト python3 バージョン)
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- dep: r-base-core
- GNU R core of statistical computation and graphics system
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- sug: hisat2
- graph-based alignment of short nucleotide reads to many genomes
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- sug: r-bioc-ebseq
- R package for RNA-Seq Differential Expression Analysis