Bash snippets
Bash snippets that are useful when doing bioinformatic jobs.
bio_embedding
installation pip install bio_embeddings[all] usage bio_embeddings …
LSTrAP
installation dependency Required Tools Bowtie2 TopHat HISAT2 Samtools SRAtools HTSeq + all …
BioPython snippets
Biopython stuff
Python snippets
Python snippets that are too long for me to remember.
Java
Java
Meme
how the internet works#bioinformatics #meme #fun #geek #coding #datascience #IT #software …
Nucleotide Sequence Visualization
👁️ Python library to plot DNA sequence features (e.g. from Genbank files) …
Nucleotide Sequence Optimization
NUPACK - analysis and design of nucleic acid structures, devices, and systems. http://nupack.org/ …
Broccoli - infer with high precision orthologous groups and pairs of proteins using a mixed phylogeny-network approach
https://github.com/rderelle/Broccoli dependency DIAMOND Fasttree manual …
DISOPRED 3 -
download ftp: http://bioinfadmin.cs.ucl.ac.uk/downloads/DISOPRED/ althought the archive marked as …
NLR-annotator
https://github.com/steuernb/NLR-Annotator Requirements MEME suite and JRE are already on GACRC …
HMMER
using HMMER with Pfam