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Bioinformatics workflow tools | RNA sequencing data analysis

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Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).

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Partek Genomics Suite

Offers an intuitive user interface and built-in workflows for a variety of genomic applications that guide researchers though every step of the analysis process. Partek Genomics Suite gives biologists, bioinformaticists, and statisticians a single, integrated solution for trustworthy results with a user-friendly interface, comprehensive workflows, and ability to support all next generation sequencing, microarray, and qPCR platforms.

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Identifies differentially expressed genes from count data or previously normalized count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene are likely to be part of the noise or represent a true differential expression.

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Datasets

Plasma autoantibody associated with basal-like breast cancer-GST4 Array Spo11-oligo mapping in Saccharomyces species (S. paradoxus, S. mikatae, S. kudriavzevii) and wild-derived S. cerevisiae strains (YPS128, UWOPS03-461.4) Convergent roles of ATF3 and CSL in chromatin control of CAF activation [RNA-seq]

Software

PhyloWidget YamAdam CRYSTALP

Users

Yahia ADNANI

Institut Gustave Roussy

Trinh Ngô

Vietnam National University, Hanoi

Vu Bich

Ho Chi Minh City University of Science

Databases

Cyanorak funRNA ITER

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