Pinned Repositories
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
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.
m6a_sarscov2
Source code and analysis repository used in "Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants"
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.
AkramMendez's Repositories
AkramMendez/custom_scripts
General repository with custom scripts for data processing, bioinformatic workflows and downstream analysis
AkramMendez/SQUAD
A brief tutorial of how to implement SQUAD for the qualitative analysis of regulatory networks
AkramMendez/AkramMendez
My personal portfolio repository
AkramMendez/AkramMendez.github.io
AkramMendez/Basset
Convolutional neural network analysis for predicting DNA sequence activity.
AkramMendez/bioconda-recipes
Conda recipes for the bioconda channel.
AkramMendez/bioinformatics-workbook
Bioinformatics Workbook repository
AkramMendez/biotools
A list of useful bioinformatics resources
AkramMendez/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
AkramMendez/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.
AkramMendez/freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
AkramMendez/m6a_sarscov2
Source code and analysis repository used in "Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants"
AkramMendez/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
AkramMendez/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
AkramMendez/Rsandbox
AkramMendez/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.
AkramMendez/HowToNotes
General Collection of my How-To Notes
AkramMendez/machine_learning
Collection of my Machine learning Notes, Scripts and Implementation Examples of common ML algorithms
AkramMendez/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
AkramMendez/nucleus
Python and C++ code for reading and writing genomics data.
AkramMendez/RSAT20y_bof
AkramMendez/sandbox
AkramMendez/scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
AkramMendez/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"
AkramMendez/TranscriptomeAssemblyTools
A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.
AkramMendez/webinR
webinR en español, conceptos básicos de R y tidyverse