Lioscro/alaska-parse

Automated and friendly RNA-seq analysis (migrated to Parse Server)

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Marval96/RNAseq_uivc

This repository is for differential expression analysis of RNAseq bulk data.

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Dragonmasterx87/Interactive-3D-Plotting-in-Seurat-3.0.0

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

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chasesmith15/Mitonuclear-SD Fork of %{name} raqmejtru/mitonuclear-sd

Investigate the role of mtDNA in the sex determination of freshwater mussels with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.

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murailab/Ponroy2020_HMG

Code to reproduce Ponroy, et. al, 2020 in Human Molecular Gentetics

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MaayanLab/Zika-RNAseq-Pipeline

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

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deeprob/rnaseq_analysis

Girirajan Lab RNA-seq analysis pipeline

Language: Python - Size: 206 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 4

iamandreatonina/Binoformatic_resources

:computer: Project for the course of Bioinformatic Resources

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JLiLab/scRNAseq_Diencephalon

Size: 343 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1

cgodatascience/circRNA

Classification of RNA-Seq samples using circRNA expression

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ecianini/single_cell_RNA-Seq

Project for the Transcriptomic course of "Bioinformatics for Computational Genomics" MSc

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adeschen/GeneiASE_Tools

R scripts to process input/output related to GeneiASE software

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rachadele/extract-geo-metadata

extract experimental metadata from GEO xml files

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ecianini/bulk_RNA-Seq

Project for the Transcriptomic course of "Bioinformatics for Computational Genomics" MSc

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kserrano109/Medicago_Rhizophagus_RNAseq

This is a repository for the publication "Spatially-Resolved, Single Cell Transcriptome Mapping of the Arbuscular Mycorrhizal Symbiosis" in which authors applied single-nuclei RNA-seq and spatial RNA-seq to the symbiosis between Medicago truncatula and Rhizophagus irregularis.

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nunofonseca/irap

integrated RNA-seq Analysis Pipeline

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wckdouglas/sequencing_tools

A python package storing different tools for different NGS operations

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pmb59/endoderm

Definitive endoderm differentiation of human ESCs in G1 phase of the cell cycle

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carpentries-incubator/FAIRification-of-RNAseq-Data

FAIRification of RNAseq Data

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aedanr/PhD-Project-2.3

Comparing hierarchical models to existing methods on simulated and recount data

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kevincjnixon/BinfTools

Useful R functions for Multi-omics analyses

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StathopoulosLab/Stathopoulos_Lab_Pipelines

A comprehensive source for Stathopoulos lab code generated and used in data analysis.

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sk-sahu/Snakeflows

Collective Snakemake workflows for easy and reproducible NGS data analysis.

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segalmicrobiomelab/lung_cancer_microbiome

Language: R - Size: 27.3 KB - Last synced at: 10 months ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 2

weng-lab/rnaseq-workflow

RNA-seq pipeline, based on the ENCODE uniform processing pipeline

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weng-lab/rnaseq-star-task

STAR task for RNA-seq workflow

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weng-lab/rnaseq-rsem-task

RSEM task for RNA-seq workflow

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weng-lab/rnaseq-kallisto-task

kallisto task for RNA-seq workflow

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weng-lab/rnaseq-bamtosignal-task

signal generation task for RNA-seq workflow

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pentalpha/r-peridot

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

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roblehmann/hts_workshop2019

Hands-on Introduction to Data Analysis for Genomics and Transcriptomics

Size: 76.6 MB - Last synced at: 11 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

jyu-theartofml/RNA_seq_diff_expression

Differential expression analysis in R for RNA sequence reads of fission yeast.

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claassenlab/Teamproject-2023

Implementation of RNA velocity for estimation of single cell transcriptomic dynamics.

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smangul1/rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

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egaffo/CirComPara

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

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mcrewcow/Pan_et_al_DFChen_IGFPL1_paper

IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

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leahkemp/running_16S_rRNA_pipeline

Trying to help a colleague get a 16s-rRNA-Sanger snakemake pipeline working.

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niqolla/ieo_RNAseq_project

eproduciton of a publication regarding gene expression in different phases of lactation in humans

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klugem/watchdog

Workflow management system for the automated and distributed analysis of large-scale experimental data.

Language: Java - Size: 193 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 12 - Forks: 4

kristiyanto/BioDepot-workflow-builder Fork of %{name} BioDepot/BioDepot-workflow-builder

GUI for creating bioinformatics workflows from Docker containers

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genepattern/Kallisto.Quant

GenePattern Notebook running Kallisto

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NehaSontakk/RNA-sequencing-fastq-to-differential-gene-expression

RNA sequencing processing and analysis to find differential expression

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ScialdoneLab/CIARA_python

Implementation of entropy of mixing algorithm in python

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sivkri/rna-Seq-ScaledLengthTPM

To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.

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sivkri/mirRNA-Seq-Analysis

scripts and resources for performing miRNA sequencing analysis using tools like mirPRo and miRDeep2. Explore the code to process reads, map them to the genome, quantify known miRNAs, identify novel miRNAs, and browse the results

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rmoffitt/GeneSetMatch

A tool for deep statistical analyses and informative visualizations of complex -omic data

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navduhan/pyseqrna

pySeqRNA: a python-based package for RNASeq data analysis

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programerkotik/Differential-Gene-Expression-Analysis

Differential gene expression analysis exercise for the course Analytical Methods in Cancer Genomics 2023. The goal is to perform analysis of RNA-Seq data.

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apredeus/multi-bacpipe

A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments

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Lihua1990/tutorials

Documenting workflows for various tasks.

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milescsmith/rnaseq_targets_pipeline

An R {targets}-based pipeline for processing and generating reports for RNAseq data

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francescopatane96/RNA-seq_Pipeline

Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...

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ishamada/CRC

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ishamada/cholangiocarcinoma

Language: R - Size: 3.91 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

BackofenLab/GraphClust-2

A pipeline for structural clustering of RNA secondary structures

Language: Python - Size: 3.54 MB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 14 - Forks: 4

schosio/CHOLAR

Automated RNA-seq pipeline for lncRNA indentification

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aedanr/PhD-Project-2.4

Assessing dIfferential expression, dispersion, distribution analyses on TCGA tumour-normal RNA-seq datasets

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nasqar/deseq2shiny

a web-based R shiny application that wraps DESeq2 R package

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bpucker/RNA-Seq_analysis

scripts for RNA-Seq analysis

Language: Python - Size: 89.8 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 8

sunyumail93/easyRNAseqDE

An R package for RNAseq differential expression analysis and visualization, in an easy and reproducible way.

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MingyiXia9717/gtex_v9_data_analysis

Analyze GTEx (V9) Oxford Nanopore long-read RNA-Seq Transcript Quantification Data

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RuzhangZhao/mixhvg

The package mixhvg uses mixture of highly variable gene selection methods to improve gene selection.

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biga94/rna-seq-msc

Language: R - Size: 1.72 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ShaneSchroeder/RNA-Sequence-Analysis-Pipeline

This series of Jupyter Notebooks will guide users through using various tools and programs to analyze experimental groups

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collaborativebioinformatics/Disease_subsetting

Colorectal cancer CMs subtyping and personalized medication recommendation based on RNA seq pathway analysis

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dohlee/snakemake-kallisto-sleuth

Kallisto-sleuth pipeline in snakemake.

Language: Python - Size: 2.93 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

LieberInstitute/PTHS_mouse

Scripts used to analyze RNAseq data from mouse models of Pitt-Hopkins Syndrome related to Phan, Bohlen et al.

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saketkc/rna-seq-snakemake

Snakemake based pipeline for RNA-Seq analysis

Language: R - Size: 54.7 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 29 - Forks: 11

RTChou/DGEclustering

An R package for RNA-seq DGE downstream automation and clustering analysis

Language: Python - Size: 160 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

frattalab/unc13a_cryptic_splicing

Figures for UNC13A paper

Language: R - Size: 112 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

ajitjohnson/arseq

An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)

Language: R - Size: 9.43 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 2

bnediction/profile_binr 📦

PROFILE RNA-seq binarization technique.

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RitchieLabIGH/iMOKA

interactive Multi Objective K-mer Analysis

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mkelly9513/OV-Project-One

Contains the code and scripts used to process and analyze the data for my analysis of super-enhancer function in ovarian cancer cells (OVCAR3) and in patient RNA-seq and Copy Number data from The Cancer Genome Atlas (TCGA). This project was published by Nat. Communications in July 2022. https://doi.org/10.1038/s41467-022-31919-8

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DeplanckeLab/Meireles-Filho_Litovchenko2019

Source code to support the paper: “Extensive tissue-specific expression variation and novel regulators underlying circadian behavior”

Language: R - Size: 786 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

safisher/ornaseq

Ontology of RNA Sequencing

Language: Makefile - Size: 118 KB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 2

Vogel-lab/Integrative-multi-omics-analyses-of-FOXG1-functions

The documented analysis of the results reported in Akol et al., 2023 as R markdowns, Galaxy histories and jupyter logs..

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SchulzLab/ORNA

Fast in-silico normalization algorithm for NGS data

Language: C++ - Size: 24.5 MB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 4

fursham-h/factR

factR: Functional Annotation of Custom-assembled Transcripts in R

Language: R - Size: 12.6 MB - Last synced at: 21 days ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

SysBioChalmers/KMG060-Systems-Biology-course

KMG060 Systems Biology course - repo for students

Language: MATLAB - Size: 22.9 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 6

OluwadareLab/EnsembleSplice

Ensemble Deep Learning for Splice Site Prediction

Language: PureBasic - Size: 163 MB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 2

dzhang32/dasper

Detecting Aberrant Splicing Events from RNA-sequencing data

Language: R - Size: 35 MB - Last synced at: 8 months ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 2

nedaghohabi/Colorectal_Cancer_Subsetting Fork of %{name} collaborativebioinformatics/Disease_subsetting

Colorectal cancer CMSs subtyping and personalized medication recommendation based on RNA seq pathway analysis

Language: Jupyter Notebook - Size: 651 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

abhay8154/SCLC-Project-Code

Analysis of SCLC Cell Lines elucidates the landscape of phenotypic heterogeneity enabling diverse SCLC subtypes.

Language: Jupyter Notebook - Size: 271 KB - Last synced at: 7 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

UBC-iGEM/wheat_RNAseq_analysis

Transcriptome Analysis of Heat and Drought-Stressed Wheat

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RuzhangZhao/scRNAseqProcess

Language: R - Size: 21.5 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

upcmarina/glioma_omics

RNA-seq analysis of glioma combination drug therapies

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williamjeong2/snakemake_RNA-seq

A repository for RNA-seq workflow

Language: R - Size: 12.9 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

AG-JY-Lab/RNA-seq-analysis

This repository maintains an end to end downstream workflow (post FASTQ alignment) of bulk RNA sequencing analysis from gene read counts to functional enrichment analysis.

Language: R - Size: 448 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

Bohdan-Khomtchouk/NGStoolkit

One-stop shop for one-click NGS analyses from the command-line

Language: Shell - Size: 16.6 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0

pentalpha/r-peridot-gui

The power of the R's differential gene expression analysis packages, with no programming required.

Language: Java - Size: 62.2 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

vondoRishi/4-RNA-seq

A slurm based pipeline for RNA-seq analysis to execute on linux clusters. Feel free to connect to visualize your RNA-seq data on the clouds

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nedaghohabi/TCGA-RNA-seq

TCGA Colorectal Cancer RNA seq Data Analysis Pipeline

Language: R - Size: 512 KB - Last synced at: almost 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

bpucker/ncss2018

Genome-wide investigation of non-canonical splice sites

Language: Python - Size: 45.9 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 3

OluwadareLab/CNNSplice

CNNSplice: Robust Models for Splice Site Prediction Using Deep Convolutional Neural Networks

Language: Python - Size: 390 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

EmoryIntegratedComputationalCore/Methods

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

Language: R - Size: 18 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 2

ArnaudFickinger/DeepSequence-PyTorch

PyTorch Implementation of DeepSequence

Language: Python - Size: 1.19 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 10 - Forks: 3

sung/HHV6-Nat-Micr-2020

A collection of custom scripts used for Gaccioli et al. Nat. Microbiol. 2020.

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Sage-Bionetworks/EvidenceAggregatedDriverRanking

Ranking methodology of potential Driver genes using multi-view feature sets

Language: Python - Size: 24.2 MB - Last synced at: 2 months ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 2

thimler/RNAseq

Assessing the effectiveness of endocrine therapy in breast cancer using RNAseq data

Language: R - Size: 12.9 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0