Updates since last release:
• budapest: Updated from Version 2.0.
→ Version 2.1: Improved handling of iTRAQ data using rje_mascot V1.2.
• comparimotif_V3: Updated from Version 3.8.
→ Version 3.8: Changed scoring of overlapping ambiguities - uses IC of all possible ambiguities. Added "Ugly" match type.
→ Version 3.9: Added xgformat=T/F : Whether to use default CompariMotif formatting or leave blank for e.g. Cytoscape [True]
• happi: Updated from Version 1.1.
→ Version 1.2: Added addclass and refined output for Host-Pathogen PPI analysis.
• pingu: Updated from Version 3.7.
→ Version 3.8: Hopefully fixed issue of Fasta file generation log output writing to wrong log file.
• qslimfinder: Updated from Version 1.4.
→ Version 1.4: Added qexact=T/F option for calculating Exact Query motif space (True) or estimating from dimers (False).
→ Version 1.5: Implemented SigV calculation. Modified extras setting.
• seqmapper: Updated from Version 1.2.
→ Version 2.0: Reworked with new Object format, new BLAST(+) module and new seqlist module.
• slimbench: Updated from Version 1.5.
→ Version 1.6: Added "simonly" to datatype - calculates both SN and FPR from "sim" data (ignores "ran") to check query bias.
→ Version 1.7: Added Benchmarking of ELM datasets without queries.
→ Version 1.8: Added Benchmarking dataset generation from PPI data and 3DID.
• slimfinder: Updated from Version 4.4.
→ Version 4.5: Minor modifications to fix sigV and sigPrime bugs. Modified extras setting. Added palindrome setting for DNA motifs.
• file_monster: Updated from Version 1.6.
→ Version 2.0: Major reworking with new object making use of rje_db tables etc. Old functions to be ported with time.
• rje_dbase: Updated from Version 2.2.
→ Version 2.3: Added construction of EnsEMBL TaxaDB sets during TaxaDB construction.
• rje_seqgen: Updated from Version 1.6.
→ Version 1.7: Modified/fixed ESTgen function to work for protein sequences.
• ned_rankbydistribution: Updated from Version 1.0.
• rje: Updated from Version 4.4.
→ Version 4.5: Modified randomString() and added stringShuffle() methods.
• rje_blast_V1: Created.
→ Version 0.0: Initial Working Compilation.
→ Version 0.1: No Out Object in Objects
→ Version 1.0: Corrected to work with blastn (and blastp)
→ Version 1.1: Added special calling for Cerberus
→ Version 1.2: Added GABLAM and GABLAMO to BlastHit
→ Version 1.3: Added GABLAM calculation upon reading BLAST results and clearing Alignment sequences to save memory
→ Version 1.4: Tidied up the module with improved logging and progress reporting. Added dbCleanup.
→ Version 1.5: Added checking for multiple hits with same name and modified BLAST_Run.hitToSeq()
→ Version 1.6: Added nucleotide vs protein searches to GABLAM
→ Version 1.7: Added nucleotide vs nucleotide searches to GABLAM
→ Version 1.8: Added local alignment summary output to ReadBLAST()
→ Version 1.9: Added BLAST -C
→ Version 1.10: Added BLAST -g
→ Version 1.11: Added gablamfrag=X : Length of gaps between mapped residue for fragmenting local hits [100]
→ Version 1.12: Altered checkDB and cleanupDB to spot index files split over multiple files (*.00.p* etc.)
→ Version 1.13: Added localcut=X : Cut-off length for local alignments contributing to global GABLAM stats) [0]
→ Version 1.14: Added blast.checkProg(qtype,stype) to check whether blastp setting matches sequence formats.
• rje_blast_V2: Created.
→ Version 2.0: Initial Compilation from rje_blast_V1 V1.14.
• rje_db: Updated from Version 0.3.
→ Version 0.4: Improved use of AutoID and added Table.autoID() method.
• rje_ensembl: Updated from Version 2.8.
→ Version 2.9: Reduced DNA chromosome downloads. Updated some species data. Added "known_by_projection" handling.
• rje_genbank: Updated from Version 0.2.
→ Version 0.3: Added reloading of features.
• rje_hmm_V1: Created.
→ Version 0.0: Initial Working Compilation.
→ Version 1.0: Working version with multiple HMM capacity
→ Version 1.1: Added hmmpfam option
→ Version 1.2: Cleaned up and debugged for rje_ensembl.ensDat()
• rje_hmm_V2: Created.
→ Version 2.0: Initial HMMER3.0 version based on Version 1.2 and RJE_BLAST 2.0.
• rje_markov: Updated from Version 2.1.
• rje_mascot: Updated from Version 1.0.
→ Version 1.1: Fixed bugs for reading in data with unmatched peptides and iTRAQ data.
→ Version 1.2: Added
• rje_menu: Updated from Version 0.2.
→ Version 0.3: Modified to work with new object types.
• rje_ppi: Updated from Version 2.5.
→ Version 2.6: Added addPPI(hub,spoke,evidence) method. Added nodelist option.
→ Version 2.7: Added tabout=T/F Output PPI data as Node and Edge tables [False]
• rje_seqlist: Updated from Version 1.1.
→ Version 1.2: Added seqshuffle option for randomising sequences.
• rje_uniprot: Updated from Version 3.12.
→ Version 3.13: Minor bug fix for link table output.
• rje_xref: Created.
→ Version 0.0: Initial Compilation.
No comments:
Post a Comment