Bioinformatics

Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.

In recent versions (can't say from exactly when), there seems to be an off-by-one error in dcc.DatePickerRange. I set max_date_allowed = datetime.today().date(), but in the calendar, yesterday is the maximum date allowed. I see it in my apps, and it is also present in the first example on the DatePickerRange documentation page.

E

Setup

Seen with latest code from git while preparing the 1.73 release on Linux, but applies to all platforms.

Expected behaviour

$ python run_tests.py test_PDB_StructureAlignment.py
Python version: 2.7.15 | packaged by conda-forge | (default, Jul 27 2018, 10:26:36) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Operating system: posix linux2
test_PDB_StructureAlignment ... ok

In pl.pca_loagings(), there should be an option to limit the number of points plotted (basically n_points from ranking)

Why: I recently used the AnnData/scanpy suite to perform some analysis on a low number of genes (less than 30, amplified by qRT-PCR).
As the number of features is less than 30 (30 being the default value for n_points in ranking(adata,*args,**kwargs), the loadings appear twice

@jonalv

As reported by @jonalv , it can be confusing what is happening when if the globber pattern does not catch any files.

The suggestion is to:

Log when the globber starts, with the pattern used
Issue a warning if the globber doesn't match any files at all

Nov	DEC	Jan
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2020	2021	2022

Bioinformatics

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Developer-Y / cs-video-courses

plotly / dash

biopython / biopython

Setup

Expected behaviour

google / deepvariant

seandavi / awesome-single-cell

danielecook / Awesome-Bioinformatics

nextflow-io / nextflow

bioconda / bioconda-recipes

OpenGene / fastp

broadinstitute / gatk

lh3 / minimap2

allenai / scispacy

lh3 / bwa

theislab / scanpy

bigdatagenomics / adam

lh3 / seqtk

scipipe / scipipe

galaxyproject / galaxy

lightaime / deep_gcns_torch

plotly / react-plotly.js

ewels / MultiQC

shenwei356 / seqkit

hail-is / hail

broadinstitute / cromwell

crazyhottommy / getting-started-with-genomics-tools-and-resources

google / nucleus

shenwei356 / csvtk

dib-lab / khmer

soedinglab / MMseqs2

samtools / htslib

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