:: DESCRIPTION
The goal of AGILE (Assembled Genome minIng pipeLinE) is to mine and annotate genes from a target genome using a set of reference genes from a closely related taxon.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hughes GM, Teeling EC.
AGILE: an assembled genome mining pipeline.
Bioinformatics. 2019 Apr 1;35(7):1252-1254. doi: 10.1093/bioinformatics/bty781. PMID: 30184049.
:: DESCRIPTION
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA.
A universal SNP and small-indel variant caller using deep neural networks.
Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24. PMID: 30247488.
:: DESCRIPTION
GenMap computes the uniqueness of k-mers for each position in the genome while allowing for up to e mismatches.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pockrandt C, Alzamel M, Iliopoulos CS, Reinert K.
GenMap: ultra-fast computation of genome mappability.
Bioinformatics. 2020 Jun 1;36(12):3687-3692. doi: 10.1093/bioinformatics/btaa222. PMID: 32246826; PMCID: PMC7320602.
:: DESCRIPTION
Apollo is the first instantaneous, collaborative genomic annotation editor available on the Web.
Web Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE.
Apollo: Democratizing genome annotation.
PLoS Comput Biol. 2019 Feb 6;15(2):e1006790. doi: 10.1371/journal.pcbi.1006790. PMID: 30726205; PMCID: PMC6380598.
:: DESCRIPTION
sgRNA online is an online tool that identifies efficient sgRNAs for CRISPR editing of mouse and human genomes. It supports both classic Cas9 and xCa9 3.7.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No
:: MORE INFORMATION
:: DESCRIPTION
CGARS is designed to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations across a set of tumor specimens or cell lines. In contrast to existing approaches, the method is invariant to any strictly monotonous transformation of the input data, which results to an insensitivity of differences in tumor purity, array saturation effects, and copy number baseline levels.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 May 1;30(9):1295-6. doi: 10.1093/bioinformatics/btu011. Epub 2014 Jan 9.
CGARS: cancer genome analysis by rank sums.
Lu X1, Thomas RK, Peifer M.
:: DESCRIPTION
GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.
:: DESCRIPTION
GenPlay is an analyzer and browser for high-throughput data . GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable tracks.
::DEVELOPER
Eric Bouhassira, Nicolas Fourel and Julien Lajugie
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Aug 31. pii: btu588.
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.
Lajugie J, Fourel N, Bouhassira EE
Bioinformatics. 2011 Jul 15;27(14):1889-93.
GenPlay, a multipurpose genome analyzer and browser.
Lajugie J, Bouhassira EE.
:: DESCRIPTION
DeepDRBP-2L is a new computational predictor for identifying DBPs, RBPs and DRBPs by combining Convolutional Neural Network (CNN) and the Long Short-Term Memory (LSTM).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Zhang J, Chen Q, Liu B.
DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug;18(4):1451-1463. doi: 10.1109/TCBB.2019.2952338. Epub 2021 Aug 6. PMID: 31722485.
:: DESCRIPTION
airpg is an Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mehl T, Gruenstaeudl M.
airpg: automatically accessing the inverted repeats of archived plastid genomes.
BMC Bioinformatics. 2021 Aug 21;22(1):413. doi: 10.1186/s12859-021-04309-y. PMID: 34418956; PMCID: PMC8379869.