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r_plot

plotting_data_viz

r_plot_ggplot2_examples

R scripts for viz and plot, collection

rcrashcourse_book

A GitBook version of the R Crash Course self-tutorials: https://colauttilab.github.io/RCrashCourse

rdptools

Collection of commonly used RDP Tools for easy building

readfq

Fast multi-line FASTA/Q reader in several programming languages

refinem

A toolbox for improving metagenome-assembled genomes.

riboviria.org

Source code for riboviria.org

rideogram

rna_seq-coculture

note from the RNA-Seq experiment of my phD (Syntrophic, Methanocella conradii, Pelotomaculum thermopropionicum)

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rpkm_rnaseq_count

RPKM for RNASeq counts

rps3_trckr

tracking of assembled rpS3 genes across metagenomes

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

rsem_tutorial

A short tutorial on how to use RSEM

rtsne

An R package for t-SNE (t-Distributed Stochastic Neighbor Embedding)

run_dbcan

Run_dbcan V2, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

sabre

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

sambamba

Tools for working with SAM/BAM/CRAM data

samsa

Programs and documentation for the SAMSA pipeline, version 1.0

samsa2

SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

scikit-learn

scikit-learn: machine learning in Python

scycdb

seeker

sem_book

An Introduction to Structural Equation Modeling

seq-scripts

scripts for sequence and feature conversion, annotation, analysis ...

seqmagick

An imagemagick-like frontend to Biopython SeqIO