Update dev to latest #4
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Adds calculateMenthu2 function for calculating version 2 MENTHU score Also fixes issue of calculateBae crashing when no 3+bp mh arms are present
…an, added scoring choice parameter to function calls, fixed cutDistances calculation for copy/paste w/o exon input, updated examples to input proper threshold depending on scoring option
Made a workaround for dealing with Genbank files missing 'number' qualifier in exon loci
…information in as.numeric calls
…orporated fast deletion algorithm calc code, added code to prevent crashes on empty microhomologies and cases where no mhs w/in 5 bp; updated v1.0 code to use fast calc; deleted old deletion frame calculation; initial commit of baeRevised function for fast deletion calc; initial commit of allsubstr for generating all common substrings between upstream and downstream
…xon counting/processing (esp. relating to 'join' statements in GenBank files)
-version update -updated sidebar links -formatting/code readability updates -temporarily disabled TALEN inputs until display issue resolved -updated input instructions -added foundation for pre-computed genes -moved fundint to HTML embed -added citation info
…nkr no longer required; Fixed getExon to deal with wiggle room better; Miscellaneous formatting and readability cleanups; fixed wonkyGenBankHandler to take apikey as input in anticipation of eventual high-throughput option
…homology that produces it; fixed deletion pattern detection to identify all possible deletions, then remove redundant deletions (i.e., deletions identical to a longer, higher-scoring microhomology; added option to specify min mh length
…omputational time; add code to process custom PAM inputs
…in the first place
Merge branch 'master' of https://github.com/Dobbs-Lab/MENTHU # Conflicts: # server.R
…ded pacakages; updated instructions, UI, and CSS; added pre-gen Cas12a nucleases; added instructions to run locally; added GitHub and Dockerhub links
…d Context to output table
Merge branch 'master' of https://github.com/Dobbs-Lab/MENTHU # Conflicts: # required2.0Functions_1.R # server.R # ui.R # www/changelog.html
…r equal to 80 nucs
…/FAQs tab, added warning about concurrent jobs/single-threading limitation, added in-frame/out-of-frame filtering options, added high-throughput command-line link in tools and downloads page
…th exon numbering in the features
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.