hussius Goto Github PK

2014-5-metagenomics-workshop

Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm

adaptor-reductor

testing out parallelization

ascii-autoencoder

TensorFlow autoencoder implementation with ASCII visualization of reconstruction progress

bcbb

Useful bioinformatics code, primarily in Python and R

bigpicture-twitterdiscourse

Companion repository to blog post "The big picture of public discourse" where we analyze Swedish Twitter data from 2015

biofreelancers

Freelance bioinformaticians directory

bra_scraper

butterfly

Code for paper "Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly" by M Celorio-Mancera et al., (2016) BMC Evolutionary Biology 16:59. doi: 10.1186/s12862-016-0627-y

courses

Course homepages for some of the courses given at SciLifeLab

curiouscrows

Team repository for the Curious Crows for Hack4Sweden 2016

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

deeplearning-biology

A list of deep learning implementations in biology

flair

A very simple framework for state-of-the-art Natural Language Processing (NLP)

gene-expression-prediction

Case study for data carpentry class on predicting differential gene expression based on genomic features

gff-phastcons-human

Scripts for obtaining max and mean PhastCons46way for a GFF of human genomic coordinates

gff-phylocsf-human

Script for scoring entries in a GFF file for coding potential using PhyloCSF score files

lstm_sandbox

Testing LSTM architectures with Valohai

meetup-lime-examples

Notebooks with examples of using LIME on tabular, text and image data, presented at Machine Learning Stockholm 2017-09-27

ml-id-lab3

proteogenomics_python

python scripts for proteogenomics analysis

publicrnaseqdata

Code for the paper "Assessing the consistency of public human tissue RNA-seq data sets" (Danielsson at al, Briefings in Bioinformatics 2015, 16 (6): 941-949)

python-sample-vscode-flask-tutorial

Sample code for the Flask tutorial in the VS Code documentation

rnasequtils

R code for working with RNA-seq count and FPKM data (filtering, visualization, outlier detection etc.)

scanbam

Script that searches a set of BAM files for RNA-seq alignments that match a provided set of peptide coordinates.

scilife-utilities

Helper scripts for NGS data processing

scilifelab

Misc code snippets for Science For Life Laboratory

scloft

shiny-imageclassif-tfslim

Shiny version of code in blog post https://www.r-bloggers.com/image-classification-in-r-using-trained-tensorflow-models/

srug190123

Code samples from Explainable ML in R talk at Stockholm R useR group 190123

stackeddae

Stacked Denoising AutoEncoder based on TensorFlow