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Bioinformatics application

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Licence:
AGPL (2) · Apache License 2.0 (6) · Artistic License (7) · Available as a standalone system (4) · Available as a standalone system or as a network license (1) · Available as a standalone system or as a network license. (2) · Available as integrated hardware & software solution. (1) · BCCA (academic use) (2) · BSD (12) · BSD (3-clause) (1) · BSD License (1) · BioLicense (1) · Biopython License (MIT/BSD style) (1) · Boost (1) · C++ (1) · CeCILL (4) · CeCILL-C license (1) · Commercial (19) · Creative Commons - Attribution-NonCommercial-ShareAlike (1) · Creative Commons - Attribution; Non-commercial 2.5 (2) · Creative Commons license (Attribution-NonCommerical). (1) · Custom Licence (8) · Free (activation required) (1) · Free evaluation (1) · Free for academic use (17) · Free for personal and academic use (1) · Free for small genomes and datasets (1) · Free of charge for non-commercial users (1) · Freely available to academic users by request: (1) · Freeware (4) · GPL (40) · GPL Boost (1) · GPL >=2 (1) · GPL 2 (2) · GPL 2.0+ (2) · GPL v3 (1) · GPLv2 (14) · GPLv3 (67) · LGPL (9) · LGPL3 (1) · Licensed for personal (1) · MIT (18) · Mozilla Public License (1) · No redistribution (1) · Non-commercial (2) · Open Source (4) · Perl artistic licence (1) · Registration required (1) · Shareware (1) · The lite version is freeware. Pro version is shareware. (1) · a network license (3) · academic (1) · and non-profit use (1) · commercial (1) · free for individual use (1) · freeware (1) · freeware license for non-commercial and non-military utilization (1) · modified BSD (1) · or as part of a site license. (3) · unknown (1) · usually available upon request (1)
Technology:
Bioinformatics methods:
Ab-inito gene prediction (1) · Adapter Removal (1) · Alignment (49) · Alignment Quality Control Sequence Analysis Visualization (1) · Alignment Analysis (4) · Alignment viewer (6) · Annotation (11) · Assembly (68) · Assembly QC (2) · Assembly editing (1) · Assembly validation (3) · Assembly visualization (9) · Basecaller (12) · Basespace (1) · Biological Contextualization (1) · Bisulfite mapping (12) · Bowtie (1) · Burrows-Wheeler (3) · ChIP seq (2) · Chromatin motif finding (1) · Chromatogram management (1) · Chromatogram viewer (2) · Classification (1) · Clustering (3) · Clustering and alignment (1) · Collapsing Methods (1) · Colorspace (11) · Contaminant filtering (1) · Copy number estimation (3) · Cost estimation (1) · Cufflinks (1) · DNA sequence analysis (5) · Data compression (8) · Database (4) · Database submission preparation (2) · De Bruijn graph (8) · Differentially expressed gene identification (7) · Empirical Bayes (1) · Error correction (13) · Exome analysis (2) · Expectation Maximization (3) · Expression profiling (3) · FM-Index (4) · Filtering (5) · Format conversion (4) · GPU (5) · Gap extension (1) · Gene Set Testing (1) · Gene fusions discovery. (1) · Genome Alignment (3) · Genome Indexing (1) · Genome browser (6) · Gibbs motif sample (1) · Hadoop (8) · Haplotype reconstruction (4) · Hash Table Based (1) · Hidden Markov Model (11) · Hybrid assembly (2) · IGV (1) · InDel discovery (7) · Integrated Solution (4) · LIMS (2) · Localized reassembly/realignment (4) · MACS (1) · MCMC (1) · Machine Learning (1) · MapReduce (5) · Mapping (104) · Methylation Calling (2) · Motif analysis (5) · Motif discovery (1) · Mutation detection (3) · Myers Bitvector Algorithm (1) · Normalization (2) · OLC (1) · PCR Primer Design (2) · Paired End (2) · Peak calling (10) · Peak detection (3) · Peak finding (3) · Pooled samples (5) · Preprocessing (2) · Primer removal (1) · Profiling short tandem repeats from short reads (1) · Programming Library (13) · Protein Binding Peak Detection (3) · QC (2) · Quality Control (3) · RNA-Seq analysis ChIP-Seq analysis (1) · Read Alignment (4) · Read Mapping and Tag Distribution Analysis (1) · Read depth analysis (2) · Read mapping (4) · Read pre-processing (1) · Read storage (1) · Regression. (1) · SAMtools (2) · SNP calling (2) · SNP discovery (10) · SWIFT Filter (1) · Sample Barcoding (5) · Scaffolding (8) · Segmentation (1) · Sequence Analysis (1) · Sequence alignment (1) · Sequence analysis (4) · Sequence parsing (2) · Sequencing Quality Control (22) · Simulation (11) · Smith-Waterman (3) · Split-read (2) · Statistical testing (4) · Statistics (5) · T-Map (1) · Tibco Spotfire (1) · Tilling (2) · Trimming (14) · Variant Calling (4) · Variant Classification (1) · Variant Mapping (1) · Variant Prioritization (3) · Viewer (7) · Visualization (29) · Workflow (3) · aligning (1) · and SNP/INDEL discovery (1) · command line tool wrappers (2) · comparative genomics (1) · contaminant filtering (1) · conversion (5) · differential expression (2) · filtering (2) · gene expression analysis (1) · gene ontology analysis (1) · general bioinformatics (1) · genetic variation annotation (5) · genome browser (1) · genomic correlations (1) · genomic overlaps (1) · genomic region matching (2) · genomics (1) · genotyping (1) · graph reduction (1) · heatmaps (1) · k-mer analysis (7) · learning algorithm (1) · mapping (1) · mapping and de-novo assembly (1) · methylation analysis (1) · miRNA Prediction (1) · miRNA analysis (Ref and Ab-initio) (1) · miRNA profiling (1) · micro assembly (2) · mixture model (1) · motif comparison (1) · motif detection (2) · motif discovery (1) · motif scanning (1) · multiple sequence alignment viewer (4) · pathway analysis (1) · peak detection (1) · phase pattern prediction (1) · profiles (1) · rRNA filtering (1) · regulatory element annotation (1) · sequence alignment (1) · sequence analysis (1) · signal (1) · species frequency estimation (1) · statistical testing (3) · structural variation discovery (2) · suffix arrays (2) · transcriptome assembly (1) · translated nucleotide search (1) · variant detection (1) · whole genome resequencing (1)
Biological domains:
Alignment (3) · Allele-specific transcription (4) · Alternative Splicing (8) · Alternative Splicing analysis (1) · Ancient DNA (1) · Assembly (3) · Bisulfite Sequencing (3) · Cancer biology (1) · ChIP-Chip (9) · ChIP-Seq (47) · ChIP-Seq Analysis (1) · ChIP-seq (3) · Chromosome Walking (1) · Clone verification (2) · Community analysis (1) · Comparative Genomics (10) · Comparative transcriptomics (2) · Copy number estimation (17) · DNA Methylation (17) · DNA-Seq (6) · De novo sequencing (3) · De novo transcriptome assembly (7) · De-novo assembly (31) · Differential Expression (4) · Differential Gene Expression (1) · Epigenomics (23) · Exome and Whole genome variant detection (4) · Exome and whole genome variant detection (2) · Functional Genomics (2) · Fusion genes (4) · Fusion transcripts (8) · Gene Expression (1) · Gene Expression Analysis (2) · Gene annotation retrieval (4) · General bioinformatics (pipeline) (8) · Genetics (1) · Genomic Assembly (3) · Genomics (85) · Genotyping (6) · High-throughput sequencing (1) · Homology (2) · InDel discovery (24) · Integrated solution (2) · Mapping (6) · MeDIP-seq (1) · Metabolic reconstruction (1) · Metagenomics (28) · Metatranscriptomics (4) · Motif analysis (5) · Motif discovery (1) · New gene discovery (1) · Next Generation Sequencing (1) · Nucleosome Positioning (1) · Pathway Analysis (1) · Personal genomics (7) · Phylogenetics (11) · Population genetics (7) · Protein structure analysis (2) · Protein structures (1) · Quality Control (6) · RNA-Seq (35) · RNA-Seq Alignment (30) · RNA-Seq Quantitation (29) · Read alignment (8) · Reference assembly (2) · Resequencing (4) · SNP Annotation (8) · SNP and indel discovery (1) · SNP discovery (68) · Sequence Analysis (1) · Sequence analysis (12) · Sequencing (11) · Small RNA (1) · Small RNA transcriptome (6) · Somatic mutations (2) · Structural variants (26) · Targeted assembly (3) · Targeted resequencing (10) · Transcription Factor Binding Site identification (3) · Transcription Factor analysis (1) · Transcription regulation (1) · Transcriptome sequencing (1) · Transcriptomics (10) · Transposable Elements (1) · Viral metagenomics (1) · Whole Genome Resequencing (9) · Whole Genome Resequencing Analysis (1) · Yeast one-hybrid (1) · Yeast two-hybrid (1) · epigenomics (1) · genotyping (1) · in vitro selection (1) · metagenomics (1) · miRNA (12) · miRNA-seq (1) · mutations and regulatory sites (2) · ncRNAs (1) · pyrotags (1) · regulatory genomics (1) · regulatory genomics epigenomics (2) · sRNA (1) · sRNA Visualisation (1) · storage (1) · systems biology (1) · transcriptomics (1)

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