nhoffman ya16sdb issues

nhoffman / ya16sdb

A curated subset of 16S rRNA sequences from NCBI

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#75 crosenth opened 2 days ago
0
Methods outline

#74 crosenth closed 3 days ago
1
Manuscript outline

#73 nhoffman opened 6 days ago
1
Option to visualize sequence distribution without the outliers in the web interface

#72 marykstewart opened 1 week ago
0
Bump scikit-learn from 1.0.2 to 1.5.0

#71 dependabot[bot] opened 1 week ago
0
Bump urllib3 from 2.2.1 to 2.2.2 in /dash

#70 dependabot[bot] opened 1 week ago
0
Add --{negative}-taxid support to Blast database(s)

#69 dhoogest opened 3 weeks ago
0
Bump jinja2 from 3.1.3 to 3.1.4 in /dash

#68 dependabot[bot] opened 1 month ago
0
Bump werkzeug from 3.0.2 to 3.0.3 in /dash

#67 dependabot[bot] opened 1 month ago
0
Bump jinja2 from 3.0.3 to 3.1.4

#66 dependabot[bot] opened 1 month ago
0
Web interface https://ya16sdb.labmed.uw.edu/ not operative?

#65 marykstewart opened 3 months ago
2
Slurm compatibility

#64 crosenth opened 5 months ago
0
Bump urllib3 from 1.26.16 to 1.26.17 in /dash

#63 dependabot[bot] closed 2 months ago
1
053 ecs stack

#62 crosenth closed 10 months ago
1
Bump scipy from 1.8.0 to 1.10.0

#61 dependabot[bot] opened 12 months ago
0
Bump joblib from 1.1.1 to 1.2.0

#60 dependabot[bot] opened 12 months ago
0
Fix actions take 2

#59 crosenth closed 1 year ago
0
Fix actions

#58 crosenth closed 1 year ago
0
Bump joblib from 1.1.0 to 1.1.1

#57 dependabot[bot] closed 1 year ago
0
requirements.txt should pin all dependencies

#56 nhoffman opened 1 year ago
0
update pipeline Docker file to use python 3.11 and bookworm base

#55 nhoffman opened 1 year ago
0
Type strain record present in latest NCBI_16S build not visible on https://ya16sdb.labmed.uw.edu/

#54 marykstewart opened 1 year ago
0
migrate to ECS

#53 nhoffman opened 1 year ago
5
Create a Dash Datatable to visualize seq_info.feather file

#52 crosenth opened 1 year ago
0
Checking my understanding of the 'type_classification' column in the new interface

#51 marykstewart closed 2 years ago
2
gateway timeouts

#50 nhoffman closed 1 year ago
2
Use the labmed classifier to illustrate species uncertainty in Dash app

#49 crosenth closed 2 years ago
2
Investigate updating the Dash app html table into a DataTable

#48 crosenth opened 2 years ago
0
bin/match_hits.py look top hit within same species

#47 crosenth closed 2 years ago
1
Add ANI tax check data to Dash app

#46 crosenth closed 2 years ago
1
Records dropped as duplicates but then 'added back' as types are absent from named_type_hits output

#45 dhoogest opened 2 years ago
2
Best match 16S type strain record in ya16sdb web interface does not match data in NGS16S output

#44 marykstewart closed 2 years ago
2
ANI annotations, dependency updates and pipeline cleanup

#43 crosenth closed 2 years ago
0
Dokku migration

#42 nkrumm closed 2 years ago
0
Create a runnable Docker image

#41 crosenth closed 2 years ago
1
Create outline for publication

#40 crosenth closed 3 days ago
1
dash app sequence records showing themselves as closet type strain (match_species)

#39 crosenth closed 3 years ago
1
Publication status of NCBI records is not current

#38 marykstewart opened 4 years ago
0
regex bug for long genome accessions

#37 dhoogest closed 4 years ago
3
genome identifier

#36 nhoffman closed 1 year ago
3
Move dash folder into its own repo

#35 crosenth closed 2 years ago
0
roll back https://github.com/nhoffman/ya16sdb/pull/31

#34 dhoogest closed 5 years ago
2
include build instructions for singularity images

#33 nhoffman opened 5 years ago
1
Distinguish 16S-only records from those that were extracted from whole genomes

#32 marykstewart opened 5 years ago
3
modifying script to incorporate couple tax cols used in ngs16s

#31 dhoogest closed 5 years ago
2
Some accession feature tables returning duplicate feature coordinates

#30 crosenth closed 2 years ago
4
generate list of species represented in filter plots

#29 nhoffman opened 5 years ago
0
add settings-example.conf

#28 nhoffman closed 5 years ago
1
review dependencies in venv vs singularity images

#27 nhoffman opened 5 years ago
1
create s3 bucket for data, automate upload of feather file

#26 nhoffman closed 5 years ago
2