资源导航

61. DEGseq: an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples; 标签：RNA-Seq Quantitation
62. FindPeaks 3.1: Findpeaks was developed to perform analysis of ChIP-Seq experiments.; 标签：ChIP-Seq
63. Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired end short reads. a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads a pattern growth approach to det...; 标签：InDel discovery, Structural variation
64. CLCbio Genomics Workbench: De novo and reference assembly SNP and small indel detection and annotation.; 标签：Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq,MiRNA, Transcriptomics
65. SeqMan NGen: Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.; 标签：Genomics, De-novo assembly, De novo transcriptome assembly,Whole Genome Resequencing, SNP discovery, InDel discovery,ChIP-Seq, RNA-Seq Alignment
66. CABOG: Celera Assembler is scientific software for DNA research.; 标签：De-novo assembly
67. Syzygy: Software to identify variants from pooled sequencing data; 标签：SNP discovery, InDel discovery
68. Tablet: Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. Tablet is a lightweight, high-performance graphical...; 标签：Genomics, Genotyping,Comparative genomics
69. GSNAP: GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program al...; 标签：RNA-Seq Alignment, DNA methylation
70. PECAN: Alignment method practical for large genomic sequences.; 标签：
71. EULER: EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are us...; 标签：
72. MetaSim: The software can be used to generate collections of synthetic reads. Générateur de reads ou de mate-pairs à partir d’un modèle d’erreur de séquençage adaptable (Sanger, 454 ou Illumina) et d’une base de données. Générateur de reads ou de mate-pairs à partir d’un modèle d’erreur de...; 标签：Metagenomics, Genomics
73. SHARCGS: SHARCGS is a suitable tool for fully exploiting novel sequencing technologies by assembling sequence contigs de novo with high confidence and by outperforming existing assembly algorithms in terms of speed and accuracy.; 标签：De-novo assembly
74. Phymm: A classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs; 标签：Metagenomics
75. SeqMap: SeqMap is a tool for mapping large amount of short sequences to the genome.; 标签：
76. PyroBayes: PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines.; 标签：SNP discovery
77. SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.; 标签：ChIP-Seq, Epigenomics
78. SeqSolve: Simple analysis of Next Generation Sequencing data.; 标签：RNA-Seq, ChIP-Seq,Transcriptomics, Small RNA transcriptome
79. VCFTools: Package for dealing with VCF (variant call format) files. Both command line and Perl API. VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working ...; 标签：
80. AMOS: AMOS is a Modular, Open-Source whole genome assembler. AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and...; 标签：de-novo assembly

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