Ecosyste.ms: Issues

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GitHub / kmayerb/tcrdist3 issues and pull requests

#112 - t-SNE visualization of distance matrix

Issue - State: open - Opened by SirKuikka 3 months ago - 1 comment

#111 - Docker container error

Issue - State: closed - Opened by SirKuikka 3 months ago - 1 comment

#110 - General Running issues.

Issue - State: open - Opened by JL-OX 3 months ago

#109 - PyPI release is outdated

Issue - State: closed - Opened by kamurani 6 months ago - 1 comment

#108 - `TCRrep._show_incomplete()` does not work

Issue - State: open - Opened by kamurani 6 months ago - 1 comment

#107 - `IndexError` when running `TCRrep` constructor

Issue - State: open - Opened by kamurani 6 months ago

#106 - Gene names should allow alternate delimiters

Issue - State: open - Opened by kamurani 6 months ago

#105 - fix typo

Pull Request - State: open - Opened by kamurani 6 months ago

#104 - compute_sparse_rect_distances replaces 0 values with -1

Issue - State: closed - Opened by liel-cohen 8 months ago - 1 comment

#103 - A to P change in CDR3 but no effect on distance

Issue - State: open - Opened by andreas-wilm 9 months ago - 2 comments

#101 - BCR distance

Issue - State: open - Opened by ChangLu92 10 months ago - 1 comment

#100 - error in import preprocess_10X

Issue - State: open - Opened by rimanpreetkaur 10 months ago - 2 comments

#99 - TRBV6-2*01?

Issue - State: open - Opened by esford3 11 months ago - 1 comment

#98 - Create python-app-py311.yml

Pull Request - State: closed - Opened by agartland 12 months ago

#97 - Add rhesus functionality

Pull Request - State: closed - Opened by kmayerb 12 months ago

#95 - Issue with metaclonotypes

Issue - State: open - Opened by jsh75 about 1 year ago

#94 - Tcrdist working with sample data but not with my data

Issue - State: closed - Opened by rutha32 over 1 year ago - 2 comments

#93 - Error with using with the newest version of python

Issue - State: closed - Opened by rutha32 over 1 year ago - 2 comments

#92 - Clustering based on aminoacid sequences alone

Issue - State: open - Opened by raphaeltrevizani over 1 year ago

#91 - Usage question

Issue - State: closed - Opened by ndrubins over 1 year ago - 1 comment

#90 - Lost Clones

Issue - State: open - Opened by TheRaspberryFox over 1 year ago - 1 comment

#89 - Poor efficiency on large dataset

Issue - State: open - Opened by pdevashishmda over 1 year ago

#88 - build_tree not working with gd TCRs

Issue - State: closed - Opened by sschattgen over 1 year ago - 1 comment

#87 - Convention N/C terminal

Issue - State: open - Opened by lisadratva over 1 year ago

#86 - Identifying which clones cluster where on a tree

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

#85 - Keep information about TCR in the TCRdist matrix

Issue - State: closed - Opened by CharlineJnnt almost 2 years ago - 2 comments

#84 - How to compare clonal similarity between different groups?

Issue - State: closed - Opened by sc30301 almost 2 years ago - 1 comment

#83 - Wrong/redundant entries in db file?

Issue - State: open - Opened by nh3 almost 2 years ago - 2 comments

#82 - Guidance on using find_metaclonotypes (specifically on bkgd_cntl_nn2 function)

Issue - State: closed - Opened by elulu3 almost 2 years ago - 1 comment

#81 - Several (more?) missing TCR chains

Issue - State: open - Opened by KJMaroney about 2 years ago

#80 - amino-acid consensus sequence

Issue - State: open - Opened by PaulDanPhillips about 2 years ago

#78 - issue with running Radius

Issue - State: open - Opened by QianhuiXu over 2 years ago - 3 comments

#77 - Memory usage of regex testing

Issue - State: open - Opened by sgp79 over 2 years ago - 2 comments

#76 - KeyError: 'pmhc_a_aa'

Issue - State: open - Opened by Tianran1 over 2 years ago - 7 comments

#75 - Installation error: File name too long

Issue - State: open - Opened by canuckafar over 2 years ago - 3 comments

#74 - tr.pw_beta vs tr.pw_cdr3_b_aa

Issue - State: open - Opened by psimps21 over 2 years ago

#73 - Problem installing due to fisher

Issue - State: open - Opened by TejasMenon over 2 years ago - 1 comment

#72 - some basic questions on tcrdist3

Issue - State: closed - Opened by SheahLinLee over 2 years ago - 3 comments

#70 - Installing with python 3.9.10, Avoid Numpy/Numba/Fisher package conflicts

Issue - State: open - Opened by kmayerb almost 3 years ago - 1 comment
Labels: documentation

#69 - Cannot import hcluster_diff, member_summ, or plot_hclust_props

Issue - State: closed - Opened by psimps21 almost 3 years ago - 6 comments

#68 - What to do with multiple prodcutive alpha or beta chains

Issue - State: closed - Opened by emjbishop almost 3 years ago - 2 comments

#67 - Installation files not found

Issue - State: closed - Opened by wukevin about 3 years ago - 7 comments

#65 - Information about metaclonotype centers

Issue - State: closed - Opened by aoki0623mriid2 about 3 years ago - 2 comments

#64 - Error in calcuating "Radius"

Issue - State: closed - Opened by aoki0623mriid2 about 3 years ago - 3 comments

#63 - [Request] Improve Documentation for tabulate

Issue - State: open - Opened by gcohenJH about 3 years ago - 2 comments

#62 - About distance threshold

Issue - State: open - Opened by showteeth about 3 years ago - 1 comment

#61 - Distances without cdr3_a_nucseq and cdr3_b_nucseq

Issue - State: closed - Opened by andreas-wilm over 3 years ago - 3 comments

#60 - Unexpected distance values for partially duplicated entries

Issue - State: closed - Opened by andreas-wilm over 3 years ago - 6 comments

#59 - Some distances silently not computed (for identical entries)

Issue - State: closed - Opened by andreas-wilm over 3 years ago - 4 comments

#58 - Added a missing argument when calling _synthesize_vj_matched_background

Pull Request - State: closed - Opened by zozo123 over 3 years ago - 4 comments

#57 - ValueError: zero-size array to reduction operation maximum which has no identity

Issue - State: closed - Opened by Lihua1990 over 3 years ago - 4 comments

#56 - Question: Combined distance matrix for alpha and beta

Issue - State: closed - Opened by andreas-wilm over 3 years ago - 8 comments

#55 - Error in "Hello tcrdist3"

Issue - State: closed - Opened by aoki0623mriid2 over 3 years ago - 3 comments

#54 - argument controls on # of synthetic genes

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

#53 - Add join.py

Pull Request - State: closed - Opened by kmayerb almost 4 years ago

#52 - ValueError: zero-size array to reduction operation maximum which has no identity

Issue - State: closed - Opened by xf78 almost 4 years ago - 1 comment

#51 - Add stop and warn for large TCRrep input

Pull Request - State: closed - Opened by kmayerb almost 4 years ago

#50 - Breadth Function

Pull Request - State: closed - Opened by kmayerb almost 4 years ago

#49 - Add path to base in test workflow 2

Pull Request - State: closed - Opened by kmayerb almost 4 years ago

#48 - Documentation of meta-clonotype discovery

Issue - State: closed - Opened by andreas-wilm almost 4 years ago - 2 comments

#47 - Code examples in documentation

Issue - State: closed - Opened by andreas-wilm almost 4 years ago - 1 comment

#46 - Add vdjtools_funcs + test + docs

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#45 - AssertionError: daemonic processes are not allowed to have children

Issue - State: closed - Opened by pixuenan about 4 years ago - 2 comments

#44 - Some of the mouse TRBV is missing

Issue - State: open - Opened by marshelma about 4 years ago - 1 comment
Labels: enhancement

#43 - Update adpt_funcs.py

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#42 - import_adaptive_file function drops subject data

Issue - State: closed - Opened by grhogg about 4 years ago - 4 comments

#41 - Added comments to ecdf about sparse encoding

Pull Request - State: closed - Opened by agartland about 4 years ago

#39 - Alpha metaclonotypes

Issue - State: closed - Opened by jeremycfd about 4 years ago - 4 comments

#38 - Change TOCtree on docs

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#37 - Add PGEN tests for mouse

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#36 - edit docs [skip ci]

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#35 - add more docs

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#34 - Parasail dependency (OSX install difficulty)

Issue - State: open - Opened by kmayerb about 4 years ago
Labels: bug

#33 - Avoid jedi==0.18.0 IPyhton crashes

Issue - State: open - Opened by kmayerb about 4 years ago
Labels: bug

#32 - A really basic example of getting started with video

Issue - State: closed - Opened by kmayerb about 4 years ago

#31 - Set to version 0.1.9

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#30 - bump to 1.8 change docker base image post Nov2020

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#29 - add tabulator

Pull Request - State: closed - Opened by kmayerb about 4 years ago - 1 comment

#28 - Add low_pass argument

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#27 - Update text

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#26 - add illustrative test

Pull Request - State: closed - Opened by kmayerb about 4 years ago

#25 - Framework

Pull Request - State: closed - Opened by kmayerb about 4 years ago - 1 comment

#24 - Add quasi-public report feature

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

#23 - Embrace sparsity

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

#22 - CSV mapper

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

#21 - Updating ECDFs and fixing warnings

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

#20 - Fix Indents on test for docs

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

#19 - Add examples for making trees ex13,14,15,16

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

#18 - Add note on compute_distances

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

#17 - Adding ECDF functions

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

#16 - Add out of memory compute functions

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

#15 - Stage ecdf

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

#14 - Update df to df_pop

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

#13 - Pgen, Olga Sampler, TCRtree

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