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Arup Ghosh - PhD Student
Open to new opportunities
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Open to new opportunities

Arup Ghosh

PhD Student
Ministry of Science and Technology • Institute of Life Sciences • Bhubaneshwar • India

Working on Immunology and Systems Biology.

RNA-seq

Preferred tools for RNA-seq analysis.

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Bowtie
Desktop

Bowtie

Aligns short read geared toward mammalian re-sequencing. Bowtie is based on a…

Aligns short read geared toward mammalian re-sequencing. Bowtie is based on a Burrows-Wheeler index based on the full-text minute-space (FM) index. It follows two steps: an initial, ungapped…

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TopHat
Desktop

TopHat

Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput…

Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. TopHat also analyzes the mapping results to identify splice junctions between exons. It can…

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Cufflinks
Desktop

Cufflinks

Assembles transcripts, estimates their abundances, and tests for differential…

Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles individual transcripts from RNA-seq reads that have…

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DESeq
Desktop

DESeq

Performs differential gene expression analysis. DEseq is a method that…

Performs differential gene expression analysis. DEseq is a method that integrates methodological advances with features to facilitate quantitative analysis of comparative RNA-seq data using shrinkage…

RefSeq
Dataset

Reference Sequence RefSeq

Offers annotation for over 95 000 genomes. RefSeq assigns informative names to…

Offers annotation for over 95 000 genomes. RefSeq assigns informative names to genes, provides some annotation for every gene found in each genome it analyzes, and supports comparative studies by…

TCGA Data Portal
Dataset

The Cancer Genome Atlas Data Portal TCGA Data Portal

Generates, analyzes, and makes available genomic sequence, expression,…

Generates, analyzes, and makes available genomic sequence, expression, methylation, and copy number variation (CNV) data on over 11,000 individuals who represent over 30 different types of cancer.…

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HISAT
Desktop

Hierarchical Indexing for Spliced Alignment of Transcript HISAT

Employs a hierarchical indexing strategy for spliced alignment. HISAT is a…

Employs a hierarchical indexing strategy for spliced alignment. HISAT is a program able to map RNA-seq reads to their origin by considering several genomic locations. It attempts to extend both…

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kallisto
Desktop

kallisto

Allows users to quantify abundances of transcripts from RNA-Seq data and target…

Allows users to quantify abundances of transcripts from RNA-Seq data and target sequences using high-throughput sequencing (HTS) reads. kallisto is based on pseudo-alignment concept to determine the…

STAR
Desktop
Web

STAR

Searches for significant approximate tandem repeats (ATR) of a given motif in a…

Searches for significant approximate tandem repeats (ATR) of a given motif in a DNA sequence. For each region of the sequence that is similar to a tandem repeat of the input motif, STAR returns a…