3938 days ago
Most Commonly used Awk by Bioinformatician
...olumn 2: awk '{x+=$2}END{print x/NR}' input.txt regex (egrep): awk '/^test[0-9]+/' input.txt calculate...'{print $1,$2}' substitution (sed is simpler in this case): awk '{sub(/test/, "no", $0);print}' input.txt...3931 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...nformatics 26(1):139-40 2010 PubMedCentral Two-stage Poisson model for testing RNA-seq data. Auer and Doe...2010 Genomic Regions Enrichment of Annotations Tool - A web service to test for over-representation of sp...3798 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
...glib.sourceforge.net/EvolSimulator A simulation test bed for hypotheses of genome...GAMETES Genetic Architecture Model Emulator for Testing and Evaluating Software: S...samples, to evaluate estimators or statistical tests, and generally to aid in the...3756 days ago
List of In-silico Binding Site Prediction Tools
...st the top servers and manual prediction groups tested at both CASP8 and CASP9.RES...with the top manual prediction groups that were tested at CASP8. The FunFOLD metho...hat allow you to extract pocket descriptors and test own scoring functions respect...3762 days ago
Next generation sequencing in R or bioconductor environment
...ayesian hierarchical t-mixture model. The following sample code uses the test data set from the above Bayes...package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. Documentat...3643 days ago
Commercial and public next-gen-seq (NGS) software
...completed will handle next-gen sequencing data. A partially implemented test version is available here XMa...he Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of...3537 days ago
Software packages for next gen sequence analysis
...completed will handle next-gen sequencing data. A partially implemented test version is available here * X...he Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of...3261 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...nted in C and uses SAMtools API; latest version should work with dipl...y can handle Illumina data; cannot test candidate indels; written in...detects somatic SNVs with multiple testing correction, uses Fisher&rs...ng applications including: carrier testing, or identification of caus...2927 days ago
Genome Assembly Tools and Software - PART1 !!
...al results showed that SWAP-Assembler is the fastest and most efficient assemblers...allel assemblers. Specially, in the scalability test, SWAP-Assembler can scales up...e in an iterative manner. From a good number of tests we see the program yields ex...2704 days ago