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- Bioinformatics application (560)
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Bioinformatics application
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Bourne shell (2) ·
C (68) ·
C# (4) ·
C++ (103) ·
CGI (1) ·
CUDA (1) ·
D (1) ·
Flash (1) ·
Fortran (1) ·
Fortran F77 (1) ·
Haskell (2) ·
Java (83) ·
Javascript (2) ·
Matlab (2) ·
Mix (2) ·
MySQL (1) ·
OCaml (1) ·
PHP (1) ·
POP-Java (1) ·
Pearl (1) ·
Perl (80) ·
Pilot Script (1) ·
Python (51) ·
R (50) ·
Ruby (5) ·
SeqAn (2) ·
Tcl (1) ·
f (1) ·
standalone version: java and some perl (1) ·
web-based (2)
AIX (1) ·
Amazon EC2 (1) ·
Cloud based (1) ·
Compaq Alpha (1) ·
Cross-Platform (4) ·
IRIX (1) ·
Linux (167) ·
Linux 64 (28) ·
Mac OS X (109) ·
Mac OS X 10.6 with Parallels Desktop (2) ·
OpenBSD (1) ·
POSIX (11) ·
Platform independent (2) ·
Solaris (9) ·
UNIX (49) ·
Windows (86) ·
Windows (Cygwin) (3) ·
Windows/Linux (1) ·
all supporting JVM (1) ·
any (3) ·
cloud (1) ·
interoperable (1) ·
platform-independent (7) ·
webserver (any) (4)
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)
454 (99) ·
ABI SOLiD (59) ·
Affymetrix (3) ·
Agilent (2) ·
Any (11) ·
ChIP-seq (2) ·
Complete Genomics (3) ·
GenePix (1) ·
Helicos (10) ·
Illumina (174) ·
Illumina? (1) ·
Ion Torrent (21) ·
Ion Torrent? (1) ·
PacBio (9) ·
Roche NimbleGen (3) ·
SOLiD (1) ·
Sanger (44) ·
Tested on Illumina. Requires short (1) ·
and 454 (1) ·
any (18) ·
pacific biosciences (1) ·
paired-end sequences. (1)
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)
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)
Showing below up to 250 results starting with #1.
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4
A
- AB Large Indel Tool
- AB Small Indel Tool
- ABBA
- ABMapper
- ABySS
- Adapter Removal
- AGE
- AGILE
- Agp2amos
- Alcovna
- ALEXA-Seq
- ALLPATHS
- Alta-Cyclic
- AMOS
- ANCHOR
- Anno-J
- ANNOVAR
- Arachne
- AREM
- Array Suite (Array Studio/Server)
- ArrayExpressHTS
- ArrayStar
- ASC
- ATAC
- Atlas Suite
- Atlas-SNP2
- Avadis NGS
B
- Bambino
- Bambus
- BAMseek
- BamTools
- BamView
- Barcode generator
- Barcrawl Bartab
- BarraCUDA
- Batman
- BayesCall
- BayesPeak
- BaySeq
- BBSeq
- Bcbio-nextgen
- BEADS
- BEAP
- BEDTools
- Belvu
- BFAST
- BFCounter
- BING
- Bionimbus
- Biopieces
- Biopython
- BiQ Analyzer
- BiQ Analyzer HT
- Bismark
- BLAST
- BLAT
- Blixem
- BOAT
- Bowtie
- BRAT
- BRCA-diagnostic
- BreakDancer
- Breakpointer
- BreakSeq
- Breakway
- BS Seeker
- BS-Seq
- BSMAP
- Btrim
- BWA
- BWA-SW
C
C cont.
- ChIPseqR
- Chipster
- ChromaSig
- ChromHMM
- CisGenome
- Cistrome
- CLCbio Genomics Workbench
- Clean reads
- CleaveLand
- CLEVER
- CloudAligner
- CloudBurst
- ClustDB
- CNANorm
- CNAseg
- CnD
- CNVer
- CnvHMM
- CNVnator
- CNVseq
- CoNAn-SNV
- ConDeTri
- ContEst
- Contrail
- CopySeq
- Coral
- CORAL (Contig Ordering Algorithm)
- Cortex
- CPTRA
- CRISP
- Crossbow
- CUDA-EC
- Cufflinks
- CummeRbund
- Curtain
- Cutadapt
D
- DecGPU
- DeconSeq
- DeFuse
- DEGseq
- DESeq
- DIAL
- DiBayes
- Diffreps
- Dindel
- DNA Baser
- DNA Chromatogram Explorer
- DNAA
- DNAzip
- DrFAST
- DSAP
- DSRC
E
- E-miR
- Ea-utils
- EagleView
- EagleView genome viewer
- ECHO
- EDENA
- EdgeR
- ELAND
- EMBF
- Epigenome
- EpiGRAPH
- ERANGE
- ERDS
- Est2assembly
- ESTcalc
- EULER
- ExomeCNV
- ExomeCopy
- Exonerate
F
F cont.
- FlowSim
- Flux
- Forge
- FragGeneScan
- FrameDP
- FreClu
- Freebayes
- FREEC
- FusionAnalyser
- FusionHunter
- FusionMap
- FusionSeq
- Fuzzypath
G
- G-Mo.R-Seq
- G-SQZ
- Galign
- Gambit
- GAMES
- GASSST
- GASV
- GATK
- GBrowse
- GeeFu
- GEM library
- GENE-Counter
- Geneious
- GeneProf
- Genomatix Mining Station (GMS)
- Genome Trax
- Genomedata
- GenomeJack
- GenomeMapper
- GenomeTools
- GenomeView
- GenomicTools
- GenoMiner
- GenoViewer
- GensearchNGS
- GenVision
- Geoseq
- GigaBayes
- GimmeMotifs
- Girafe
- Gk arrays
- GMAP
- Gnumap
- Goby framework
- Golden Helix
- Goseq
- GPS
- GPSeq
- GRS
- GSNAP
