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BED file manipulation bioinformatics software tools

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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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BEDTools
Desktop

BEDTools

A software suite for the comparison, manipulation and annotation of genomic…

A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of…

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TCGA2BED
Desktop

TCGA2BED

Aims to search and retrieve The Cancer Genome Atlas (TCGA) data. TCGA2BED…

Aims to search and retrieve The Cancer Genome Atlas (TCGA) data. TCGA2BED converts them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion…

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NGSUtils
Desktop

NGSUtils

A suite of software tools for manipulating data common to next-generation…

A suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. With modules that operate from FASTQ pre-processing through…

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NGS-Bits
Desktop

NGS-Bits

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal…

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal experiments. NGS-Bits is separate into four steps: (1) gather information from raw reads, (2) map reads, (3) extract variant…

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pybedtools
Desktop

pybedtools

A flexible Python software library for manipulating and exploring genomic…

A flexible Python software library for manipulating and exploring genomic datasets in many common formats. pybedtools provides an intuitive Python interface that extends upon the popular BEDTools…

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PileLine
Desktop

PileLine

Implements a flexible command-line toolkit providing specific support to the…

Implements a flexible command-line toolkit providing specific support to the management, filtering, comparison and annotation of genomic position (GP) files produced by next generation sequencing…

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ChIPseek
Web

ChIPseek

A web-based tool for ChIP data analysis providing summary statistics in graphs…

A web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses.

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pybio
Desktop

pybio

Permits users to proceed to basic genomics operations. pybio offers motif…

Permits users to proceed to basic genomics operations. pybio offers motif sequence searches functions. It can classify alternative polyadenylation site-pair.

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