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naobservatory
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mgs-pipeline
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Update the taxonomy and reference DBs
#65
jeffkaufman
closed
1 month ago
1
Added Leung 2021 (Metasub study of air in metro systems across the globe)
#64
simonleandergrimm
closed
5 months ago
0
Simon rosario 2018
#63
simonleandergrimm
closed
5 months ago
0
Ran Prussin 2019 through mgs-pipeline.
#62
simonleandergrimm
closed
5 months ago
0
Fixing a small bug in ribo_frac.
#61
simonleandergrimm
closed
5 months ago
3
dashboard: update instructions for pushing data live
#60
jeffkaufman
closed
6 months ago
0
Simon add belstrom 2017
#59
simonleandergrimm
closed
6 months ago
3
Riboreads fails on bioproject PRJNA396840, sample SRR5892185
#58
simonleandergrimm
closed
1 month ago
1
ribofrac: fix typo
#57
jeffkaufman
closed
6 months ago
1
Fix import-accession and metadata for Grumaz 2016
#56
lennijusten
closed
7 months ago
1
classifier-comparison: first cut at classifier framework
#55
jeffkaufman
closed
7 months ago
0
Pipeline: Allow parallelizing at the sample level
#54
jeffkaufman
closed
7 months ago
2
running prepare-dashboard.sh on main without other edits.
#53
simonleandergrimm
closed
7 months ago
6
Reformatted all .py scripts with black. Deleted bioprojects/PRJNA774620/metadata/prepare-metadata.py
#52
simonleandergrimm
closed
7 months ago
1
Added check.sh to the repository. Checks if all Python scripts are formatted with black.
#51
simonleandergrimm
closed
7 months ago
0
alignments: additionally align against human genome
#50
jeffkaufman
closed
7 months ago
0
Added locations to Bohl 2022 (Cambodia) and Wu 2020 (Wuhan). Reran prepare_dashboard.sh
#49
simonleandergrimm
closed
7 months ago
6
Add plasma papers
#48
lennijusten
closed
7 months ago
1
alignments: align all reads, not just hvreads
#47
jeffkaufman
closed
7 months ago
3
Bowtie: mask low-complexity sequences
#46
jeffkaufman
closed
8 months ago
0
Automatically add sample metadata when importing new bioprojects
#45
lennijusten
closed
7 months ago
2
build bowtie: avoid duplicates
#44
jeffkaufman
closed
8 months ago
0
bowtie: minor fixes after running bowtie across all existing data
#43
jeffkaufman
closed
8 months ago
0
dashboard: more reworking
#42
jeffkaufman
closed
8 months ago
0
dashboard: stop using data.js, and pull individual json files instead
#41
jeffkaufman
closed
8 months ago
0
dashboard: start breaking out per-bioproject counts
#40
jeffkaufman
closed
8 months ago
0
Dashboard: check in first half of Tisza 2023 data
#39
jeffkaufman
closed
8 months ago
1
Alignments: add a new pipeline stage that runs Bowtie2
#38
jeffkaufman
closed
8 months ago
0
bowtie: make map for interpreting genome ids
#37
jeffkaufman
closed
8 months ago
2
Add a script for reprocessing all the bioprojects in parallel
#36
jeffkaufman
closed
7 months ago
2
Simon bowtie2 db
#35
simonleandergrimm
closed
8 months ago
3
dashboard: fix bug where we were getting zero counts for human-infecting viruses
#34
jeffkaufman
closed
8 months ago
0
Add ribofrac data to dashboard
#33
lennijusten
closed
8 months ago
3
implement readlengths
#32
jeffkaufman
closed
8 months ago
2
Add new stage, samplereads
#31
jeffkaufman
closed
8 months ago
0
Ribofrac: Check for empty files and skip samples with zero reads
#30
lennijusten
closed
8 months ago
3
Added kraken assignment to creation of hvreads.
#29
simonleandergrimm
closed
8 months ago
1
Save "nan" for ribofrac when sample has zero reads
#28
lennijusten
closed
9 months ago
0
dashboard: add ribofrac data
#27
lennijusten
closed
8 months ago
1
ribofrac: add dashboard files
#26
lennijusten
closed
9 months ago
1
Get rRNA fraction with fast ribocounts()
#25
lennijusten
closed
9 months ago
0
Adding feature to ribocounts that saves non-rRNA read IDs
#24
lennijusten
closed
9 months ago
1
Run Langenfeld data
#23
dp-rice
closed
9 months ago
4
Add ribocounts dashboard data
#22
lennijusten
closed
9 months ago
2
Add ribcounts to sample metadata for dashboard deployment
#21
lennijusten
closed
9 months ago
0
Add Lagenfeld 2022
#20
dp-rice
closed
10 months ago
1
Adding Riquelme 2022 to dashboard, attempt 2
#19
willbradshaw
closed
10 months ago
3
Read counting isn't correct
#18
jeffkaufman
closed
10 months ago
1
Prepared metadata for Riquelme 2022
#17
willbradshaw
closed
10 months ago
0
Adding RiboDetector to MGS pipeline
#16
lennijusten
closed
10 months ago
2
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