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A workflow for omic data analysis

12342 tools classified by omic technologies, applications and analytical steps

Omic Technologies

Omic Data

Epigenomic software tools and databases

Epigenomics

Here, we surveyed web-based bioinformatics platforms, software tools and databases for the analysis of…

Transcriptomic software tools and databases

Transcriptomics

Here, we surveyed web-based bioinformatics platforms, software tools and databases for the analysis of…

Metabolomic software tools and databases

Metabolomics

Here, we surveyed web-based bioinformatics platforms, software tools and databases for the analysis of…

Fluxomic software tools and databases

Fluxomics

Here, we surveyed web-based bioinformatics platforms, software tools and databases for the analysis of…

Biological pathway analysis software tools and databases

Pathway analysis

Here, we surveyed bioinformatics software tools and databases for analysing biological pathways.

Genome editing software tools and databases

Genome editing

Here, we surveyed web-based bioinformatics platforms, software tools and databases for genome editing…

RNA interference data and software tools

RNA interference

Here, we surveyed databases and bioinformatics software tools to design RNAi reagents and analyze RNAi screen…

Phenomic data and software tools

Phenomics

Here, we surveyed databases and bioinformatics software tools for phenomic analysis.

Drug discovery software tools and databases

Drug discovery

Drug discovery software tools and databases

Synthetic biology tools

Synthetic biology

Software tools and databases for synthetic biology.

Metabolic engineering software tools and databases

Metabolic engineering

Metabolic engineering software tools and databases

Biomolecular structure software tools and databases

Biomolecular structure

Biomolecular structure software tools and databases

Health and medical research software tools and databases

Health sciences

Health and medical research software tools and databases

Immunology software tools and databases

Immunology

Immunology software tools and databases

Biomedical text mining software tools and databases

Text-mining

Biomedical text mining software tools and databases

Tools

Most Recent Tools

new
OMIC_12679
Somatic CNA detection

CloneCNA

A bioinformatics tool for efficiently addressing these issues and automatically detecting…

A bioinformatics tool for efficiently addressing these issues and automatically detecting clonal and subclonal somatic copy number alterations from heterogeneous tumor samples. CloneCNA fully explores the log ratio of read counts between paired…

new
OMIC_12678
Tumor purity and…

MuSE

A somatic point mutation caller for tumor-normal paired samples in next-generation…

A somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data. MuSE models the evolution of the reference allele to the allelic composition of the matched tumor and normal tissue at each genomic locus. To improve…

new
OMIC_12677
Single-cell RNA-seq

scVEGs

An algorithm for single-cell RNA-seq data to determine significant variably expressed…

An algorithm for single-cell RNA-seq data to determine significant variably expressed genes (VEGs) using a gene expression variation model (GEVM). scVEGs utilizes the relation between coefficient of variation (CV) and average expression level to…

new
OMIC_12676
CRISPR/Cas9

Cas-Analyzer

A JavaScript-based instant assessment tool for high-throughput sequencing data for genome…

A JavaScript-based instant assessment tool for high-throughput sequencing data for genome edited cells. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server,…

Most Popular Tools

popular
OMIC_05565
Venn diagrams

VENNY

An interactive tool for comparing lists with Venn Diagrams.

An interactive tool for comparing lists with Venn Diagrams.

popular
OMIC_00090
Somatic SNV detection

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It consists of…

A suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format), BCFtools (Reading/writing BCF2/VCF/gVCF files and…

popular
OMIC_00535
Transcription factor data

footprintDB

Predicts transcription factors which bind a specific DNA site or motif and DNA motifs or…

Predicts transcription factors which bind a specific DNA site or motif and DNA motifs or sites likely to be recognized by a specific DNA-binding protein.

popular
OMIC_02198
Variant effect prediction

SNPdryad

A computational method that can predict deleterious effect of amino acid substitutions…

A computational method that can predict deleterious effect of amino acid substitutions occurred in human proteins. SNPdryad outperforms other leading algorithms in accurately predicting deleterious nsSNPs.

Community

User reviews

cnorvell's avatar image

cnorvell

Best Semantic Graph Database on the Market. The Gruff visualization tool is the best for Graph…

View AllegroGraph page

Joseale Romero's avatar image

Joseale Romero

Indispensable to work with BAM/SAM alignment files. Sorts, indexes, views...

View SAMtools page

Joseale Romero's avatar image

Joseale Romero

Good short read alignment. Fairly easy to use.

View Burrows-Wheeler Aligner page

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