claraqin neonMicrobe issues

claraqin / neonMicrobe

Processing NEON soil microbe marker gene sequence data into ASV tables.

GNU Lesser General Public License v3.0

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issues

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CyVerse test using `analyze-neon-greatplains-16s.R`

#45 KaiZhuPhD opened 3 years ago
3
Install Rhtslib error

#44 KaiZhuPhD closed 3 years ago
2
Batch structure

#43 claraqin closed 3 years ago
0
created R package structure

#42 claraqin closed 3 years ago
1
downloadRawSequenceData: include progress bar, and skip download if file already exists

#41 claraqin closed 3 years ago
1
Meta reliant utils

#40 claraqin closed 3 years ago
0
Ensure that code involving NEON soil data products still works

#39 claraqin closed 3 years ago
4
Error in downloadRawSoilData()

#38 claraqin closed 3 years ago
5
Better associations between metadata and sequence data

#37 claraqin closed 3 years ago
6
Replace filename-parsing code with metadata-matching code in all vignettes

#36 claraqin closed 3 years ago
1
Have params printed to screen conspicuously at some point

#35 claraqin closed 3 years ago
1
Change output directory structure

#34 claraqin closed 3 years ago
1
Help Clara test her GitHub notifications!

#33 claraqin closed 3 years ago
1
Add verbose flag to downloadRawSequenceData()

#32 claraqin closed 3 years ago
1
Revise "dada2_to_phyloseq_[its/16s].Rmd" (aka "Add Environmental Variables") vignettes to match new metadata format

#31 claraqin closed 3 years ago
1
Make pipeline robust to changing file naming conventions

#30 claraqin closed 3 years ago
2
Metadata/downloading QC checklist

#29 claraqin opened 3 years ago
6
can't knit vignette download-neon-data

#28 lstanish closed 3 years ago
4
Instructions for pipeline testing

#27 claraqin opened 3 years ago
3
Pipeline testing on Windows

#26 KaiZhuPhD opened 3 years ago
8
Include variable name descriptions in workflow

#25 claraqin closed 3 years ago
0
Follow R package conventions for directory structure

#24 claraqin closed 3 years ago
2
Make remove_unmatched_files() robust to differences in file naming convention

#23 claraqin closed 3 years ago
1
Refer to downloaded sequence data using metadata, not list.files

#22 claraqin closed 4 years ago
0
Fastq files must be in fastq.gz format for sequence processing pipeline

#21 claraqin closed 3 years ago
2
Update the vignettes to remove chimeras AFTER merging sequence tables

#20 claraqin closed 4 years ago
5
Option to exclude legacy data and other dataQF tags

#19 claraqin closed 3 years ago
3
organizeRawSequenceData should sort ITS/16S based on metadata

#18 claraqin closed 4 years ago
2
Sequence downloading functions should utilize neonUtilities::zipsByURI

#17 claraqin closed 3 years ago
2
Create paired-end options for the ITS sequence processing vignette

#16 claraqin opened 4 years ago
0
Create vignette for sensitivity analysis

#15 claraqin closed 3 years ago
0
Simplify directory construction using system commands

#14 zoey-rw closed 4 years ago
2
Soil database construction cannot handle missing data

#13 zoey-rw closed 4 years ago
3
began workaround

#12 claraqin closed 4 years ago
0
Separate runs

#11 claraqin closed 4 years ago
0
Test

#10 claraqin closed 4 years ago
0
Some fastq file URLs return 404 error

#9 claraqin closed 4 years ago
1
Make selective downloading more robust

#8 claraqin closed 4 years ago
7
DADA2::filterAndTrim removes majority of ITS reads

#7 claraqin closed 4 years ago
3
Error tolerance of cutadapt should also be a parameter

#6 claraqin opened 4 years ago
3
Mixed orientation of reads in R1 and R2 files

#5 claraqin closed 4 years ago
2
Read fastq.gz file

#4 KaiZhuPhD closed 4 years ago
1
Project management

#3 KaiZhuPhD closed 4 years ago
0
New server setup data download

#2 yyachung closed 4 years ago
4
Data folders

#1 KaiZhuPhD closed 4 years ago
1