akrammendez Goto Github PK

akrammendez

My personal portfolio repository

akrammendez.github.io

basset

Convolutional neural network analysis for predicting DNA sequence activity.

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics-workbook

Bioinformatics Workbook repository

biotools

A list of useful bioinformatics resources

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

custom_scripts

General repository with custom scripts for data processing, bioinformatic workflows and downstream analysis

data-science-ipython-notebooks

Data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe, Keras), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines.

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

howtonotes

General Collection of my How-To Notes

m6a_sarscov2

Source code and analysis repository used in "Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants"

machine_learning

Collection of my Machine learning Notes, Scripts and Implementation Examples of common ML algorithms

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nucleus

Python and C++ code for reading and writing genomics data.

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rsandbox

rsat20y_bof

sandbox

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

squad

A brief tutorial of how to implement SQUAD for the qualitative analysis of regulatory networks

squadproject

Dynamic network models has been used in biological contexts to represent complex regulatory interactions between molecules. Discrete Boolean methods are often used as a first modeling approximation. However in some biological contexts they are not sufficient to represent some behaviors as that which depends on threshold activation or molecular gradients. In these cases, ordinary differential equations are preferred but their application need the knowledge of kinetic parameters. Here we describe a continuous ODE system called Standardized Qualitative Analysis of Dynamics (SQUAD) as a first approximation to simulate continuous models without the need of kinetic parameters.

transcriptomeassemblytools

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.

webinr

webinR en español, conceptos básicos de R y tidyverse