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biocore
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metagenomics_pooling_notebook
Jupyter notebooks to assist with sample processing
MIT License
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Make columns in [Bioinformatics] w/boolean values case-insensitive.
#212
charles-cowart
closed
1 day ago
1
Boolean values in [Bioinformatics] section are now case-insensitive.
#211
charles-cowart
closed
1 day ago
1
Removed non_host_removal & fraction_non_human from output
#210
charles-cowart
closed
2 days ago
2
Remove legacy columns from seqpro output.
#209
charles-cowart
closed
1 day ago
1
Validate against duplicate sample-info-file columns
#208
charles-cowart
opened
2 weeks ago
1
Dev metaT notebook
#207
RodolfoSalido
opened
3 weeks ago
0
replicate [Data] columns reimplemented like Katharoseq
#206
charles-cowart
opened
1 month ago
0
migrate post-metapool validation into metapool
#205
charles-cowart
opened
1 month ago
0
update seqpro
#204
charles-cowart
opened
1 month ago
0
[Bioinformatics] section validation
#203
charles-cowart
opened
1 month ago
0
Possible removal of BarcodesAreRC column
#202
charles-cowart
closed
1 month ago
8
WIP Updates
#201
charles-cowart
opened
2 months ago
0
Incorporate matrix tube sample accession into amplicon notebook v2
#200
charles-cowart
closed
2 months ago
4
Removed legacy atropos-and-bowtie2 setting.
#199
charles-cowart
closed
2 months ago
0
remove 'atropos-and-bowtie2' as an option from metapool and seqpro
#198
charles-cowart
closed
2 months ago
1
update examples to current katharo naming scheme.
#197
charles-cowart
opened
2 months ago
0
Remove tube+liquid mass from config
#196
AmandaBirmingham
closed
2 months ago
0
Add support for an optional file containing sequence counts.
#195
charles-cowart
opened
2 months ago
0
remove manual creation of sample-sheet objects
#194
charles-cowart
opened
2 months ago
3
Add optional karatho control columns in [Data] section
#193
charles-cowart
closed
2 months ago
3
Incorporate matrix tube sample accession into amplicon notebook
#192
cbrenchy
closed
2 months ago
2
Support new metatranscriptomic columns
#191
charles-cowart
closed
3 months ago
1
overlapping BLANK naming when dealing with multiple projects
#190
cbrenchy
opened
3 months ago
1
validate_plate_df function should allow for arguments specifying sample_name column in metadata
#189
maddyambre
opened
3 months ago
0
Ensure TRUE/FALSE is caught when validating sample-sheets.
#188
charles-cowart
opened
3 months ago
2
replace generic 'this doesn't appear to be a valid sample-sheet' error.
#187
charles-cowart
opened
3 months ago
0
incorporates the latest changes from production testing.
#186
charles-cowart
closed
3 months ago
3
Sanity check does not hold for replicates
#185
charles-cowart
closed
4 months ago
0
Adjust error message for missing SheetType and SheetVersion parameters
#184
charles-cowart
opened
4 months ago
0
reimplemented total count w/seqtk
#183
charles-cowart
closed
4 months ago
0
Add lane-extraction from a sample-sheet
#182
charles-cowart
closed
4 months ago
0
Removed sanity-check to support plate-level rep
#181
charles-cowart
closed
4 months ago
0
bugfix for declaring new metatranscriptomic class
#180
charles-cowart
closed
4 months ago
2
seqpro updated to pass through columns
#179
charles-cowart
closed
4 months ago
3
Added MetatranscriptomicTypeV10
#178
charles-cowart
closed
4 months ago
9
Added total_biological_reads_r1r2.
#177
charles-cowart
closed
4 months ago
2
'NovaSeq X' and 'NovaSeq X Plus' need to be added to list of sequencers with Forward i5 index direction (OTHER_SEQUENCERS)
#176
RodolfoSalido
opened
5 months ago
1
Fixes #172
#175
charles-cowart
closed
5 months ago
0
Fixes #173
#174
charles-cowart
closed
5 months ago
1
make_sample_sheet() missed samplesheet validation errors that load_sample_sheet() catches.
#173
RodolfoSalido
closed
5 months ago
1
Metatranscriptomic samplesheets should also have 'contains_replicates' boolean in Bioinformatics.
#172
RodolfoSalido
closed
5 months ago
0
Update attribute names, convert tabs to spaces.
#171
charles-cowart
closed
5 months ago
1
Minor change to capitalize some column names.
#170
charles-cowart
closed
6 months ago
1
Add matrix tube sample accession support for amplicon notebooks.
#169
RodolfoSalido
opened
6 months ago
2
multiple project iSeq readcount merge
#168
RodolfoSalido
opened
6 months ago
2
lint fixes
#167
AmandaBirmingham
closed
6 months ago
0
redo of tellseq_syndna changes on updated background
#166
AmandaBirmingham
closed
5 months ago
0
redo of tellseq_syndna changes on new dev background
#165
AmandaBirmingham
closed
6 months ago
0
Give AmpliconSampleSheet a SheetType.
#164
charles-cowart
closed
6 months ago
0
Tellseq syndna notebook
#163
AmandaBirmingham
closed
6 months ago
0
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