资源导航

41. SAMMate: GUI for processing SAM/BAM and BED files. The software allows users to accurately estimate gene expression scores using short reads originating from both exons and exon-exon junctions, to generate wiggle files for visualization in UCSC genome browser, and to generate an alignment statis...; 标签：RNA-Seq Quantitation
42. NGS-DesignTools: Tools to assist in designing deep sequencing experiments for haplotype reconstruction and structural variant breakpoint detection; 标签：Structural variation, RNA-Seq Quantitation
43. TASE: Rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets.; 标签：RNA-Seq Quantitation
44. BBSeq: Tool for analyzing RNA-Seq data to analyze gene expression; 标签：RNA-Seq Quantitation
45. ConDeTri: ConDeTri is a content dependent read trimming software for Illumina/Solexa sequencing data; 标签：RNA-Seq, DNA-Seq, Genomics
46. PALMA: We present a novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm -- called PALMA -- tunes the parameters of the model such that true alignments sco...; 标签：RNA-Seq Alignment
47. Sim4cc: Cross-species spliced alignment of ESTs to genomes; 标签：RNA-Seq Alignment, Comparative genomics
48. GENE-Counter: GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression; 标签：RNA-Seq
49. FDM: Detects differential transcription in RNA-Seq data; 标签：RNA-Seq Quantitation
50. MAYDAY: Extensible platform for visual data exploration and interactive analysis and provides many methods for dissecting complex transcriptome datasets.; 标签：RNA-Seq
51. MapNext: MapNext provides four mainly analysis: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcriptomic reads, (iii) SNP detection and calculation of SNP frequency from population sequences, and (iv) storage of result data into database to make it available for ...; 标签：SNP discovery, RNA-Seq Alignment
52. S-MART: S-MART manages your RNA-Seq and ChIP-Seq data.; 标签：RNA-Seq, ChIP-Seq
53. Chipster: User-friendly NGS data analysis software with built-in genome browser and workflow functionality. Chipster includes tools for ChIP-seq, RNA-seq, miRNA-seq and MeDIP-seq analysis, and functionality for exome-seq and CGH-seq will soon be added.; 标签：ChIP-Seq, RNA-Seq, MiRNA-Seq,MeDIP-Seq
54. SpliceTrap: SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data. Instead of full transcript quantification, SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is in...; 标签：Alternative Splicing, RNA-Seq Quantitation, RNA-Seq
55. GeneProf: GeneProf is a web-based, graphical software suite and database resource for high-throughput-sequencing experiments (RNA-seq and ChIP-seq).; 标签：RNA-Seq, ChIP-Seq
56. STAR: Ultrafast universal RNA-seq aligner; 标签：RNA-Seq, Transcriptome
57. GenomicTools: GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. A variety of mathematical operations between sets of genomic regions is implemented thereby enabling the prototyping of computational pipe...; 标签：Genomics, ChIP-Seq, RNA-Seq
58. Bort: Bort parses Blast output and quantifies hits by contig and read counts.; 标签：RNA-Seq Quantitation
59. RECOUNT: Probabilistic tag count error correction for next generation sequencing data (Solexa/Illumina).; 标签：RNA-Seq Quantitation
60. SeqSaw: A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.; 标签：RNA-Seq, Alternative Splicing

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