BioNumPy

Python library for array programming on biological datasets. Documentation available at:

[BioNumPy @BioNumPy]

And we're now published in Nature Methods 🥳 Full article here: https://t.co/Mngh9CcCsr

[Geir Kjetil Sandve @SandveGeir]

Finally biologists can also use numpy (array programming). Handling e.g. DNA and protein sequences with convenience and speed, like physicists and machine learners for decades have worked with numerical data: https://t.co/06MjAmBINx (1/3)

[BioNumPy @BioNumPy]

Finally, a cool example showing that there are fewer mapped reads on average around genomic variants. Check out this colab if you want to try out the examples: https://t.co/wOG7g5GLIP

[BioNumPy @BioNumPy]

BioNumPy has been updated with changes that make it a lot easier to work with genomic intervals and data on a reference genome 😀

Here are a few cool examples to illustrate the new stuff:

[BioNumPy @BioNumPy]

.. or around transcription factor peak summits. Here we plot the pileup for reads on the positive and negative strand, and clearly see the pileups we expect around the summit.

[BioNumPy @BioNumPy]

@vsbuffalo BioNumPy has some support for gtf files, but have not yet defined a complete set of abstractions for them. Would love suggestions for useful methods!

[BioNumPy @BioNumPy]

@vsbuffalo BioNumPy tries to give a uniform interface for parsing common bioinformatics formats. Keeping the header information from input through analysis to output is under progress and will be in place for BioNumPy 0.3 https://t.co/WFKcM41wfA

[BioNumPy @BioNumPy]

Day 5/5 of short BioNumPy examples: Finding the most common kmers in a FASTQ-file.

Try out the code here: https://t.co/rdpLLUVoQh

Check out our documentation for more cool examples: https://t.co/sgcXIUI6OX🤠

[BioNumPy @BioNumPy]

Day 4 of small #BioNumPy examples: Sequence matching (searching for a sequence in a set of reads).

Try out the code here: https://t.co/C4rEJPIR6i

[BioNumPy @BioNumPy]

Day 3 of small BioNumPy examples: Plotting the mean base qualities across reads.

Try out the code here: https://t.co/7IEzYwcqlY

.. and remember to follow us for daily examples😋

[BioNumPy @BioNumPy]

Day 2/5 of small BioNumPy examples: Motif matching.

We download a motif from Jaspar, compute max motif score per read in a FASTQ file and plot a histogram of the scores.

Run the code here: https://t.co/1eOe5bee2c

[BioNumPy @BioNumPy]

Every day this week, we'll share a small example of how BioNumPy can be used.

First out: FASTQ filtering

(try out the code yourself here: https://t.co/s0fVxmoWub)

.. and remember to follow us for daily updates ☺️