Ecosyste.ms: Issues

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GitHub / JamieHeather/stitchr issues and pull requests

#39 - Add option to read FASTA automatically into additional-genes.fasta

Issue - State: open - Opened by JamieHeather 11 months ago
Labels: enhancement

#38 - Restriction sites

Pull Request - State: closed - Opened by tmixon19030 almost 1 year ago - 2 comments

#37 - Specify databases location

Issue - State: closed - Opened by dcarbajo about 1 year ago - 5 comments

#36 - Better input fields

Pull Request - State: closed - Opened by tmixon19030 about 1 year ago - 2 comments

#32 - CDR1/2

Issue - State: closed - Opened by dstcr over 1 year ago - 2 comments

#31 - Compatibility of stitchr with Windows

Issue - State: closed - Opened by naity over 1 year ago - 5 comments
Labels: bug, enhancement

#30 - thimble function gives an error for LEADER sequence when stitching TCR

Issue - State: closed - Opened by rita-the-scientist over 1 year ago - 3 comments

#29 - Add -cite option to stitchr

Issue - State: closed - Opened by JamieHeather about 2 years ago
Labels: enhancement

#28 - Improve % of perfectly replicated CDR3s when using a NT CDR3

Issue - State: open - Opened by JamieHeather about 2 years ago
Labels: enhancement

#27 - Alternative non-templated codon usage?

Issue - State: open - Opened by JamieHeather about 2 years ago
Labels: enhancement

#26 - Possible to use custom species (non-human/non-mouse)?

Issue - State: closed - Opened by slukowski over 2 years ago - 1 comment

#25 - TRDV2 error

Issue - State: closed - Opened by zacharyzale over 2 years ago - 2 comments
Labels: bug

#24 - Lower case CDR3 amino acid characters cause an error

Issue - State: closed - Opened by JamieHeather over 2 years ago - 1 comment
Labels: bug

#23 - J/C region broken in certain genes in skip/extra gene mode

Issue - State: closed - Opened by JamieHeather over 2 years ago - 1 comment
Labels: bug

#22 - Simplifying output / silent mode

Issue - State: closed - Opened by EdGreen21 almost 3 years ago - 1 comment
Labels: enhancement

#21 - Thimble GUI example files throw error

Issue - State: closed - Opened by EdGreen21 almost 3 years ago - 1 comment
Labels: bug

#20 - Merging v0.9.0 dev changes into main (big update)

Pull Request - State: closed - Opened by JamieHeather almost 3 years ago

#19 - Add capacity for gamma/delta TCR stitching

Issue - State: closed - Opened by JamieHeather almost 3 years ago
Labels: enhancement

#18 - Post-TRAC stop codon nucleotides resulting in frameshifts in TRA-TRB paired sequences

Issue - State: closed - Opened by JamieHeather almost 3 years ago - 1 comment
Labels: bug

#17 - 2021-05-17: updating readme/adding logo

Pull Request - State: closed - Opened by JamieHeather over 3 years ago

#16 - UserWarning error in Thimble

Issue - State: closed - Opened by JamieHeather almost 4 years ago - 1 comment
Labels: bug

#15 - Make length of J substring match shorter/changeable in command line

Issue - State: closed - Opened by JamieHeather almost 4 years ago - 1 comment
Labels: enhancement

#14 - Give warning if only gene level specified when multiple alleles known

Issue - State: closed - Opened by JamieHeather over 4 years ago
Labels: enhancement

#13 - Dev merge: upgrade to Python 3, fixes truncated TRAC bug

Pull Request - State: closed - Opened by JamieHeather over 4 years ago

#12 - Add python3 compatibility

Pull Request - State: closed - Opened by MLAxelrod over 4 years ago - 1 comment

#11 - Terminal 2 TRAC nucleotides missing from output

Issue - State: closed - Opened by JamieHeather over 4 years ago
Labels: bug

#10 - Upgrade to python 3

Issue - State: closed - Opened by JamieHeather over 4 years ago
Labels: enhancement

#9 - 2019-08-14: stitchr v0.3 and thimble v0.1 - high throughput stitching!

Pull Request - State: closed - Opened by JamieHeather over 5 years ago - 1 comment

#8 - Merging testmouse branch on to master

Pull Request - State: closed - Opened by JamieHeather over 5 years ago

#7 - exits with an error but zero status code

Issue - State: closed - Opened by carandraug over 5 years ago - 1 comment

#6 - fails weirdly if it can't find tcr data

Issue - State: closed - Opened by carandraug over 5 years ago - 2 comments

#5 - Make stitchr work on mouse TCRs

Issue - State: closed - Opened by JamieHeather over 5 years ago - 1 comment
Labels: enhancement

#4 - Can't get demo TCRs or help functions to print

Issue - State: closed - Opened by wyattmcdonnell over 5 years ago - 2 comments

#3 - stitch errors if -a option is not specified

Issue - State: closed - Opened by carandraug over 5 years ago - 2 comments

#2 - none of the examples in README are valid

Issue - State: closed - Opened by carandraug over 5 years ago - 1 comment

#1 - errors if J interface is not found

Issue - State: closed - Opened by carandraug over 5 years ago - 1 comment