arosenfeld/immunedb issues and pull requests

#105 - Bump pymysql from 0.9.3 to 1.1.1

Pull Request - State: open - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#104 - Bump gunicorn from 21.0.1 to 22.0.0

Pull Request - State: open - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#103 - Bump eventlet from 0.34.2 to 0.35.2

Pull Request - State: open - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#102 - Bump scipy from 1.5.4 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#101 - Bump numpy from 1.19.5 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 3 comments
Labels: dependencies

#100 - Bump bottle from 0.12.16 to 0.12.20

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#99 - Running ImmuneDB using Singularity

Issue - State: open - Opened by Liamck almost 3 years ago

#98 - Can immnuedb support TRD and TRG?

Issue - State: open - Opened by haoqing12 almost 3 years ago

#97 - Error when running igblast.sh with IGL and IGK options (human)

Issue - State: closed - Opened by Elyes88 over 3 years ago - 1 comment

#96 - new file added

Pull Request - State: closed - Opened by areensh over 3 years ago - 1 comment

#95 - Bump eventlet from 0.24.1 to 0.31.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#94 - Bump bottle from 0.12.16 to 0.12.19

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 2 comments
Labels: dependencies

#93 - metadata is missing and issue with --trim

Issue - State: closed - Opened by areensh about 4 years ago - 6 comments

#92 - error when running run_igblast.sh

Issue - State: closed - Opened by linquynus over 4 years ago - 2 comments
Labels: bug

#91 - Retrieving Full BCR sequence

Issue - State: closed - Opened by ajulienla about 5 years ago - 2 comments

#90 - problem with vj identification

Issue - State: closed - Opened by aurelBZH about 5 years ago - 5 comments

#89 - use of compressed fastq

Issue - State: closed - Opened by aurelBZH about 5 years ago - 2 comments

#88 - V-identity should break ties for similar clonal collapsing

Issue - State: open - Opened by arosenfeld over 5 years ago
Labels: enhancement

#87 - BASENAME question

Issue - State: closed - Opened by cornelius-agrippa over 5 years ago - 3 comments

#86 - new file added

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

#85 - MemoryError when identifying large fasta(q) files (>6GB)

Issue - State: open - Opened by azuretimm almost 6 years ago - 10 comments
Labels: bug

#84 - Sample name update fails for switched names

Issue - State: open - Opened by arosenfeld almost 6 years ago
Labels: bug

#83 - Trees should be set to null if no sequences are included

Issue - State: closed - Opened by arosenfeld almost 6 years ago
Labels: bug

#82 - Configurable API endpoint in Docker

Issue - State: closed - Opened by arosenfeld about 6 years ago - 1 comment
Labels: enhancement

#81 - Error in docs - I think...

Issue - State: closed - Opened by bcorrie about 6 years ago - 1 comment

#80 - Add node ID to lineages

Issue - State: closed - Opened by arosenfeld about 6 years ago
Labels: enhancement

#78 - without SQL analysis

Issue - State: closed - Opened by BlingArida about 6 years ago - 1 comment

#77 - Add ability to delete samples

Issue - State: closed - Opened by arosenfeld over 6 years ago - 1 comment

#76 - Add instance count to CloneStats

Issue - State: closed - Opened by arosenfeld almost 7 years ago - 1 comment
Labels: enhancement, wontfix

#75 - Custom metadata

Issue - State: closed - Opened by arosenfeld about 7 years ago
Labels: enhancement

#74 - V-ties in genes with different lengths

Issue - State: open - Opened by arosenfeld about 7 years ago
Labels: bug

#73 - CDR3 length inconsistent under local alignment

Issue - State: closed - Opened by arosenfeld over 7 years ago
Labels: bug

#72 - instances_in_subject wrong

Issue - State: closed - Opened by arosenfeld almost 8 years ago
Labels: bug

#71 - Clone Functionality with Indels

Issue - State: closed - Opened by arosenfeld about 8 years ago
Labels: bug

#70 - Rename date to timepoint

Issue - State: closed - Opened by arosenfeld about 8 years ago - 1 comment
Labels: enhancement

#69 - Exporting indels

Issue - State: closed - Opened by arosenfeld about 8 years ago - 1 comment
Labels: enhancement

#68 - Normalized Copy Number

Issue - State: closed - Opened by arosenfeld over 8 years ago
Labels: enhancement, wontfix

#66 - Add search by CDR3 for clones and sequences

Issue - State: open - Opened by arosenfeld over 8 years ago
Labels: enhancement

#65 - Metadata from CSV/TSV

Issue - State: closed - Opened by arosenfeld over 8 years ago - 1 comment
Labels: enhancement

#64 - Argument parser defaults

Issue - State: closed - Opened by arosenfeld over 8 years ago
Labels: enhancement

#63 - Export Selection Pressure

Issue - State: closed - Opened by arosenfeld almost 9 years ago - 1 comment
Labels: enhancement

#62 - Store selection pressure as a separate table

Issue - State: closed - Opened by arosenfeld almost 9 years ago - 2 comments
Labels: enhancement

#61 - Inconsistent clone mutation positions

Issue - State: closed - Opened by arosenfeld almost 9 years ago
Labels: bug

#60 - Collapse reset should delete samples

Issue - State: closed - Opened by arosenfeld almost 9 years ago
Labels: enhancement

#59 - Padding incorrect for trimmed sequence

Issue - State: closed - Opened by arosenfeld almost 9 years ago - 1 comment
Labels: bug

#58 - Add subject_id to CloneStats

Issue - State: closed - Opened by arosenfeld almost 9 years ago - 1 comment
Labels: enhancement

#57 - IGHV Ties

Issue - State: closed - Opened by arosenfeld about 9 years ago
Labels: bug

#56 - Indel count incorrect

Issue - State: closed - Opened by arosenfeld about 9 years ago
Labels: bug

#55 - Trimmed sequence info in local alignment

Issue - State: closed - Opened by arosenfeld about 9 years ago
Labels: enhancement, wontfix

#54 - Multiprocessing

Issue - State: closed - Opened by arosenfeld about 9 years ago
Labels: enhancement

#53 - Separate clone stats and selection pressure calculation

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#52 - Separate baseline and mutation calculations

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: duplicate, enhancement

#51 - V extent is wrong for indel clones

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: bug

#50 - Import models at proper locations

Issue - State: closed - Opened by arosenfeld over 9 years ago
Labels: enhancement

#49 - Phred score wrong when indels corrected

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: bug

#48 - Filter clone trees by subject

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#47 - Fail if metadata is missing

Issue - State: open - Opened by arosenfeld over 9 years ago
Labels: bug

#46 - Add -std=c99 to extra_compile_args

Issue - State: closed - Opened by arosenfeld over 9 years ago
Labels: bug

#45 - Protparam for clones

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement, wontfix

#44 - Mutation/clone export size threshold

Issue - State: closed - Opened by arosenfeld over 9 years ago
Labels: enhancement, wontfix

#43 - Collapsing should not erase unmodified samples

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#42 - Tree node annotations

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#41 - API call for studies should index by date

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#40 - Anchor update

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#39 - Clone ID in Collapse

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: bug

#38 - Sequence hash and unique check

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement, invalid

#37 - Custom metadata path

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#36 - Exporting

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: bug

#35 - Baseline failures should be logged

Issue - State: open - Opened by arosenfeld over 9 years ago
Labels: bug

#34 - Unique Sample Names

Issue - State: closed - Opened by arosenfeld over 9 years ago
Labels: wontfix

#33 - Worker IDs

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#32 - Exporting clip should use clone germline

Issue - State: closed - Opened by arosenfeld over 9 years ago
Labels: bug

#31 - Add v-gene length filter to identification

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement, wontfix

#30 - Filtering stop codons from clones

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement, wontfix

#29 - Exporting fastq

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: enhancement

#28 - Sample date should be mandatory

Issue - State: closed - Opened by arosenfeld over 9 years ago - 1 comment
Labels: bug

#27 - Make sldb_clones multiprocessed by bin

Issue - State: closed - Opened by arosenfeld almost 10 years ago - 1 comment
Labels: enhancement

#26 - Unique Sequence Constraint

Issue - State: closed - Opened by arosenfeld almost 10 years ago - 1 comment
Labels: bug, wontfix

#25 - V-Usage Grouping Multiple Samples

Issue - State: closed - Opened by arosenfeld almost 10 years ago - 1 comment
Labels: bug

#24 - Unique CDRs in Clone Assignment

Issue - State: closed - Opened by arosenfeld almost 10 years ago
Labels: enhancement

#23 - Large V-ties

Issue - State: closed - Opened by arosenfeld almost 10 years ago - 1 comment
Labels: bug

#22 - Mutation stats are not populated

Issue - State: open - Opened by arosenfeld almost 10 years ago
Labels: bug

#21 - Modification should trigger mutation update

Issue - State: closed - Opened by arosenfeld almost 10 years ago - 1 comment
Labels: bug, wontfix

#20 - Duplicate Sequences

Issue - State: closed - Opened by arosenfeld almost 10 years ago - 1 comment
Labels: bug

#19 - Valid Read Count

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: bug

#18 - NoResult Alignments

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement, wontfix

#17 - Indel Detection Changes

Issue - State: closed - Opened by arosenfeld about 10 years ago
Labels: enhancement, wontfix

#16 - Clone Export Total Rows

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement

#15 - Partial Sequences in Clones

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: bug

#14 - Identification File Sort

Issue - State: closed - Opened by arosenfeld about 10 years ago
Labels: enhancement

#13 - Logging

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement

#12 - Fix Clone Export

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: bug

#11 - Pre-calculate Mutations

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment

#10 - V & J length too long for short CDR3s

Issue - State: closed - Opened by arosenfeld about 10 years ago
Labels: bug

#9 - Identification Duplicate Check

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement

#8 - Sequence Unique Constraint

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement

#7 - J Gene Ties

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: bug

#6 - Remove pRESTO references

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement

#5 - Custom Germlines

Issue - State: closed - Opened by arosenfeld about 10 years ago - 1 comment
Labels: enhancement

#4 - Move _get_args from api.queries to api.rest_service

Issue - State: closed - Opened by arosenfeld about 10 years ago
Labels: enhancement

GitHub / arosenfeld/immunedb issues and pull requests