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biopython-cn

Biopython Tutorial Chinese Translation

books

:books: Books worth reading

capr

CapR calculates probabilities that each RNA base position is located within each secondary structural context for long RNA sequences.

ceres

Computational correction of copy-number effect in CRISPR-Cas9 essentiality screens

chirp-seq

clipper

A tool to identify CLIP-seq peaks

comet

CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

demeter2

Inference of gene dependency from RNAi screening datasets.

dna-methylation-analysis

my notes on DNA methylation analysis (arrays and sequencing data)

dplyr

Dplyr: A grammar of data manipulation

eqtl-brain

eQTL (single and Meta analysis of Brain tissue)

gatk

GATK Official Release Repository

ipanda

insilico Pathway Activation Network Decomposition Analysis (iPANDA) package. Owned by Insilico Medicine Inc. iPANDA is a pathway analysis method that aids interpretation of large-scale gene expression data. The method introduced here includes coexpression analysis and gene importance estimation to robustly identify relevant pathways and biomarkers for patient stratification.

ipsa

This is IPSA package light version

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

jvarkit

Java utilities for Bioinformatics

krux

Automatically exported from code.google.com/p/krux

mdseq

MDSeq: Gene expression mean and variability analysis for RNA-seq counts

mlr

Machine Learning in R

ngs

Next-Gen Sequencing tools from the Horvath Lab

ocrf

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pu-learning

Positive and unlabeled learning wrappers for scikit-learn

rna2essential

rna expression to essential genes

rnabind

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.

scikit-learn

scikit-learn: machine learning in Python

scikit-learn-videos

Jupyter notebooks from the scikit-learn video series

scikit-sos

A Python implementation of the Stochastic Outlier Selection algorithm

scrna.seq.course

Analysis of single cell RNA-seq data course, Cambridge University, UK