Golob-Minot geneshot issues

Golob-Minot / geneshot

MIT License

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issues

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Refactor CAG refinement process

#45 sminot closed 4 years ago
1
Add PSI-BLAST

#44 sminot opened 4 years ago
0
Refactor CAG construction using Zarr

#43 sminot closed 4 years ago
0
Add rRNA prediction

#42 sminot closed 3 years ago
1
Refactor assemble abundances

#41 sminot closed 4 years ago
0
Improve efficiency of corncob analysis

#40 sminot closed 4 years ago
2
Add jaccard distances

#39 sminot closed 4 years ago
1
Corncob results currently only readable from Python 3.8

#38 prihoda closed 4 years ago
3
Perform meta-analysis of corncob results by gene annotation

#37 sminot closed 4 years ago
0
Add pairwise distances to results HDF5

#36 sminot closed 4 years ago
0
Add metaPhlAn2 to HDF5

#35 sminot closed 4 years ago
0
Set annotation databases by default

#34 sminot opened 4 years ago
2
Bugfixes and enhancements

#33 sminot closed 4 years ago
1
Automatically validate output file format

#32 sminot closed 4 years ago
0
Index the /annot/gene/all table

#31 sminot closed 4 years ago
1
Add q-values to the corncob outputs

#30 sminot closed 4 years ago
1
Refactor output HDF5 files

#29 sminot closed 4 years ago
0
Check for empty inputs

#28 sminot opened 4 years ago
0
Sample richness metrics

#27 sminot closed 4 years ago
0
add antiSMASH for synthetic pathway identification

#26 jgolob opened 4 years ago
1
Skip `CombineReads` for specimens with one read pair

#25 jgolob closed 4 years ago
2
Include outputs to support visualization

#24 sminot closed 4 years ago
0
download_sra searches by project ID not accession

#23 jgolob closed 4 years ago
2
Add gene summary metrics

#22 sminot closed 4 years ago
0
Composition

#21 jgolob closed 4 years ago
1
Add option to set minimum CAG size for running stats

#20 sminot closed 4 years ago
1
Include the taxonomy in the summary HDF5

#19 sminot closed 4 years ago
1
Fix bugs publishing locally

#18 sminot closed 4 years ago
1
Add details to gene annotation table

#17 sminot closed 4 years ago
0
Refactor to construct CAGs via de novo assembly

#16 sminot closed 4 years ago
0
Fix duplicated genes

#15 sminot closed 4 years ago
1
Add MetaBAT2

#14 sminot closed 4 years ago
2
Make sure that reads have matching headers

#13 sminot closed 4 years ago
1
Require SRA entries to be PAIRED

#12 sminot closed 4 years ago
1
Make Entrez queries single-threaded

#11 sminot closed 4 years ago
1
Script which will automatically download paired-end FASTQ data from an NCBI BioProject

#10 sminot closed 4 years ago
1
Add nf_preprocess code

#9 sminot closed 4 years ago
0
Support both _de novo_ assembly-based and reference-based gene-level analysis

#8 sminot closed 4 years ago
2
Nextflow implementation

#7 sminot closed 5 years ago
0
Explicitly require that all reads are aligned to the human genome

#6 sminot closed 3 years ago
3
Support FTP as an file target

#5 sminot closed 4 years ago
1
Example config file

#4 sminot closed 4 years ago
1
Download and index the human genome

#3 sminot closed 4 years ago
1
Add example config file

#2 sminot closed 4 years ago
1
remove human reads task

#1 jgolob closed 4 years ago
2