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http://www.reddit.com/r/bioinformatics/
A subreddit dedicated to bioinformatics, computational genomics and systems biology.
Proper citation: reddit (RRID:SCR_011983) Copy
http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas
Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.
Proper citation: Genboree Workbench (RRID:SCR_011864) Copy
https://bioinf.eva.mpg.de/ibis/
An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads.
Proper citation: Ibis (RRID:SCR_011865) Copy
Waikato University, is a comprehensive university in Hamilton, New Zealand. The university was established in 1964, and has an additional campus located in Tauranga.
Proper citation: University of Waikato; Hamilton; New Zealand (RRID:SCR_011745) Copy
http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://www-huber.embl.de/users/anders/HTSeq/doc/count.html
Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: htseq-count (RRID:SCR_011867) Copy
University was established in 1816 and is the largest university in Poland. One of the top Polish universities.
Proper citation: University of Warsaw; Warsaw; Poland (RRID:SCR_011747) Copy
http://pages.cs.wisc.edu/~bsettles/abner/
A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.
Proper citation: ABNER (RRID:SCR_011868) Copy
Public research university on the outskirts of Coventry between the West Midlands and Warwickshire, England. It was founded in 1965 as part of a government initiative to expand higher education.
Proper citation: University of Warwick; Coventry; United Kingdom (RRID:SCR_011748) Copy
http://www.eecs.ucf.edu/~xiaoman/SIOMICS/SIOMICS.html
A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.
Proper citation: SIOMICS (RRID:SCR_011990) Copy
A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.
Proper citation: LitInspector (RRID:SCR_011870) Copy
http://derisilab.ucsf.edu/data/microarray/index.html
A public source for microarray protocols and software.
Proper citation: Microarrays.org (RRID:SCR_011992) Copy
An open-source program for doing molecular docking.
Proper citation: AutoDock Vina (RRID:SCR_011958) Copy
http://cran.r-project.org/web/packages/vegan/index.html
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Proper citation: vegan (RRID:SCR_011950) Copy
http://www.exelixis-lab.org/software.html
A tool for delimiting species on phylogenies and evolutionary placements.
Proper citation: PTP (RRID:SCR_011952) Copy
https://github.com/MikkelSchubert/adapterremoval
Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.
Proper citation: AdapterRemoval (RRID:SCR_011834) Copy
Public research university in Knoxville, Tennessee.
Proper citation: University of Tennessee Knoxville; Tennessee; USA (RRID:SCR_011714) Copy
http://graphics.med.yale.edu/trim/
A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.
Proper citation: Btrim (RRID:SCR_011836) Copy
http://www.pacific.edu/pharmchem
Proud to be a premier California school for pharmacy and health sciences, The Thomas J. Long School was founded in 1955 and offers professional and graduate degrees in pharmacy, physical therapy and speech-language pathology. Located on the campus of the University of the Pacific in Stockton, California, our school's pharmacy and health science programs are accredited by the respective national accreditation entities. We provide an outstanding academic environment that combines didactic and experiential learning as a focal point for our students. We hold academic affiliations with major medical centers, teaching hospitals, and related practice settings in support of our educational programs. We prepare our students for lifelong success in health careers by providing an excellent student-centered learning environment. Our students develop leadership skills and a strong commitment to their professions and to society. We support outstanding professional and graduate teaching, research and other scholarly activities, and services as a means of achieving our mission.
Proper citation: University of the Pacific School of Pharmacy and Health Sciences (RRID:SCR_011727) Copy
http://www.cs.helsinki.fi/u/lmsalmel/coral/
An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.
Proper citation: Coral (RRID:SCR_011849) Copy
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