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- 17:40, 26 December 2019 Headless BioUML (hist) [2,393 bytes] Ilya Kiselev (Talk | contribs) (Created page with "Headless BioUML (or Shell BioUML) is a version of standalone BioUML application without graphic user interface. It allows manipulation with data from repository, import files,...")
- 14:33, 27 November 2019 Contributors (hist) [34 bytes] Ilya Kiselev (Talk | contribs) (Created page with "* BioUML team * geneXplain")
- 22:33, 2 May 2019 Site prediction (hist) [5,530 bytes] Semyonk@dote.ru (Talk | contribs) (Created page with "Prediction of TF-binding sites of given TF in whole genome or in given chromosome fragment or in ChIP-Seq dataset. Sites are predicted by different Position Weight Matrix (PWM...")
- 19:11, 4 April 2019 RAGOUT (hist) [1,000 bytes] Sergey Pintus (Talk | contribs) (Created page with "==Description== Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (con...")
- 19:47, 27 March 2019 QUAST (hist) [1,569 bytes] Sergey Pintus (Talk | contribs) (Created page with "==What it does== QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. If you have one or multiple genome assemblies, you can a...")
- 14:24, 27 March 2019 SPAdes stats (hist) [471 bytes] Sergey Pintus (Talk | contribs) (Created page with "==What it does== Using the output of SPAdes (a pair of fasta file and stat file for each of the contigs and scaffolds), it produces a coverage vs. contig plot. Each dot repre...")
- 14:16, 27 March 2019 Filter SPAdes output (hist) [376 bytes] Sergey Pintus (Talk | contribs) (Created page with "==What it does== Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under ...")
- 15:58, 26 March 2019 New BioStore (hist) [5,632 bytes] Nikita Mandrik (Talk | contribs) (draft of the new biostore page)
- 19:53, 25 March 2019 SPAdes (hist) [1,764 bytes] Sergey Pintus (Talk | contribs) (Created page with "==What it does== SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades...")
- 18:20, 25 March 2019 Fastx clip (hist) [616 bytes] Sergey Pintus (Talk | contribs) (Created page with "==What it does== This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. ==Clipping Illustration== [[File:https://toolshed.g2.bx.psu.edu/repository/...")
- 17:15, 25 March 2019 Fastq mcf (hist) [3,798 bytes] Sergey Pintus (Talk | contribs) (Created page with "=Introduction= fastq-mcf attempts to: * Detect & remove sequencing adapters and primers * Detect limited skewing at the ends of reads and clip * Detect poor quality at...")
- 12:23, 20 March 2019 ChIP-seq Analysis (hist) [3,594 bytes] Semyonk@dote.ru (Talk | contribs) (Created page with "=== Description === Processing raw Chip-seq data and calculation of quality control metrics for TFBS datasets and AUCs-applications ==== FPCM and FNCM ==== To determine FPCM ...")
- 14:41, 14 March 2019 Optimization document (hist) [9,070 bytes] Elena Kutumova (Talk | contribs) (Created page with "A brief description of the optimization methods implemented in BioUML as well as their application to non-linear models of biochemical processes based on the minimization of s...")
- 14:20, 14 March 2019 Оptimization document (hist) [9,066 bytes] Elena Kutumova (Talk | contribs) (Created page with "A brief description of the optimization methods implemented in BioUML as well as their application to non-linear models of biochemical processes based on the minimization of s...")
- 12:57, 13 March 2019 SBGN examples (hist) [382 bytes] Ilya Kiselev (Talk | contribs) (Created page with "These diagrams demonstrate BioUML capabilities in creation and work with SBGN Diagrams are taken from SBGN [http://sbgn.github.io/sbgn/examples#insulin-signalling| web site]. ...")
- 11:25, 13 March 2019 Tools Comparison (hist) [1,636 bytes] Ilya Kiselev (Talk | contribs) (Created page with "Here we collect information about similar software and their features in comparison with BioUML.")
- 09:20, 13 March 2019 Optimization examples (hist) [10,832 bytes] Elena Kutumova (Talk | contribs) (Created page with "A brief description of the optimization methods implemented in BioUML can be found in the section Optimization problem.")
- 19:32, 12 March 2019 Expression mapping (hist) [1,114 bytes] Sergey Pintus (Talk | contribs) (Created page with "With analysis Add expression values one can color diagrams that visualize gene pathways according to their expression in microarray or RNAseq experiments")
- 16:36, 12 March 2019 Biouml.plugins.cytoscape (plugin) (hist) [348 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:35, 12 March 2019 Biouml.plugins.machinelearning (plugin) (hist) [493 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:35, 12 March 2019 Biouml.plugins.mirprom (plugin) (hist) [364 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:35, 12 March 2019 Biouml.plugins.pathfinder (plugin) (hist) [287 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:35, 12 March 2019 Ru.biosoft.exception (plugin) (hist) [166 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:35, 12 March 2019 Ru.biosoft.jobcontrol (plugin) (hist) [162 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:35, 12 March 2019 Find master regulators in mutated network (TRANSPATH(R)) (workflow) (hist) [397 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Mapping to ontologies for multiple gene sets (HumanPSD(TM)) (workflow) (hist) [1,637 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Mapping to ontologies and comparison for two gene sets (HumanPSD(TM)) (workflow) (hist) [407 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Mapping to ontologies (HumanPSD(TM)) (workflow) (hist) [497 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Gene set enrichment analysis HumanPSD (Illumina probes) (workflow) (hist) [1,602 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Gene set enrichment analysis HumanPSD (Gene table) (workflow) (hist) [1,330 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Gene set enrichment analysis HumanPSD (Agilent probes) (workflow) (hist) [1,814 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Gene set enrichment analysis HumanPSD (Affymetrix probes) (workflow) (hist) [1,610 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Cross-species mapping to ontologies, using orthologue information (HumanPSD(TM)) (workflow) (hist) [600 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 ChIP-Seq - Identify and classify target genes (HumanPSD(TM)) (workflow) (hist) [689 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Sign test (analysis) (hist) [732 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Table imputation (analysis) (hist) [707 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Quantile normalization (analysis) (hist) [550 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Mappability histogram (analysis) (hist) [722 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:34, 12 March 2019 Treatment Simulation (analysis) (hist) [2,456 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Infer network (analysis) (hist) [565 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Enhance Score (analysis) (hist) [701 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Diagram to user hub collection (analysis) (hist) [777 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Convert diagram to pairs (analysis) (hist) [784 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Convert diagram to Transpath (analysis) (hist) [880 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Regression analysis advanced (analysis) (hist) [2,393 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Classification analysis advanced (analysis) (hist) [2,364 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Cytoscape network format (hist) [512 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Split VCF by regulation (analysis) (hist) [627 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Select keynodes with top targets (analysis) (hist) [876 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
- 16:33, 12 March 2019 Pharmaceutical Compounds analysis (hist) [1,611 bytes] BioUML wiki Bot (Talk | contribs) (Automatic synchronization with BioUML)
