Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: rna-sequencing
JannesSP/ont_simsig
Project to simulate simple Oxford Nanopore Technologies RNA signals
Language: Python - Size: 98.4 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0
guma44/GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
Language: Jupyter Notebook - Size: 13.3 MB - Last synced: 6 days ago - Pushed: 26 days ago - Stars: 130 - Forks: 49
novoalab/EpiNano
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
Language: Python - Size: 5.12 GB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 102 - Forks: 32
LRB-IIMCB/ninetails
An R package for finding non-adenosine residues in poly(A) tails of ONT direct RNA sequencing reads
Language: R - Size: 9.65 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 3
SciLifeLab/NGI-RNAseq Fork of nf-core/rnaseq 📦
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
Language: Groovy - Size: 45.4 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 51 - Forks: 42
mrdanieleze/Genomic-Sequence-Comparison-Code-GSCC-
This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!
Language: Python - Size: 26.4 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 0
tluquez/QUARS
QUAlity control for RNA_Seq, a nextflow pipeline
Language: Groovy - Size: 2.58 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 2
Rupak09/ImageGuardian
Image Encryption using GENOMICS (Central Dogma algorithm).
Language: Python - Size: 182 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
sunyumail93/PipeRNAseq
A comprehensive pipeline for RNAseq data analysis
Language: Shell - Size: 107 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 16 - Forks: 1
bce99/m6A-RNA-Modification-Prediction
:dna: Prediction of m6A RNA modifications on all SG-NEx direct RNA-Seq samples
Language: Jupyter Notebook - Size: 17.7 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0
ptdolan/CirQuestDSV
Annotation and Analysis of Deep Sequencing Variants from CirSeq
Language: R - Size: 483 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 3 - Forks: 1
matteocereda/GSECA
Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data
Language: R - Size: 56.4 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 0
marislab/create-pptc-pdx-oncoprints
As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.
Language: R - Size: 67.4 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 2
10adavis/DESeq2_fGSEA_Flow
This repo is a template for running differential gene expression analysis of RNA-seq count data followed by gene set enrichment analysis. This workflow is run in R using Rmarkdown. It is based around the popular R packages, DESeq2, fGSEA, and others.
Language: R - Size: 7.22 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0
nrohani/SARS-CoV-2
DisCoVering potential candidates of RNAi-based therapy for SARS-CoV-2 using computational methods
Language: Python - Size: 2.49 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
frydaddy07/STICS-Portfolio
A portfolio of the work done during COMP 260 during S17 at Wesleyan University
Language: Python - Size: 7.81 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0
pk7zuva/ADFinder
A script to find adaptor and index sequence in raw small RNA sequencing data
Language: Shell - Size: 8.79 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
Lioscro/alaska-parse
Automated and friendly RNA-seq analysis (migrated to Parse Server)
Language: JavaScript - Size: 4.02 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 1 - Forks: 0
KrasnitzLab/RAIDS
Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
Language: R - Size: 7.11 MB - Last synced: 11 days ago - Pushed: 7 months ago - Stars: 5 - Forks: 4
cspinetta/bio-tp
TP Bioinformatica - UTN FRBA
Language: Scala - Size: 14.2 MB - Last synced: 10 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 0
niqolla/ieo_RNAseq_project
eproduciton of a publication regarding gene expression in different phases of lactation in humans
Language: TeX - Size: 22.6 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
eleni-chr/long-read-RNA-seq-plotting-suite
Various functions to inspect, extract, and visualise long-read RNA-seq data.
Language: MATLAB - Size: 72.3 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1
smaegol/nanotail
R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions
Language: R - Size: 20.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 7 - Forks: 5
darelab2014/Dinopore
DInoPORE: Direct detection of INOsines in native RNA with nanoPORE sequencing
Language: R - Size: 39.6 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 9 - Forks: 2
safisher/ornaseq
Ontology of RNA Sequencing
Language: Makefile - Size: 118 KB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2
ZihengZZH/survival-analysis
discovering novel biomarkers in RNA-Seq data with tree-based models and survival analysis
Language: Python - Size: 1.01 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 4 - Forks: 2
vniems/BD-Lithium
A collection of source codes for network-based multi-omics analysis using integrated genome-wide association studies (GWAS) and transcriptomic data to identify genetic contribution into lithium response in patients with bipolar disorder (BD).
Language: HTML - Size: 1.54 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0
lweasel/piquant
A pipeline to assess the quantification of transcripts.
Language: Python - Size: 3.33 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 19 - Forks: 4
thokall/RNA-decay
Analysis of RNA decay data set
Language: R - Size: 724 KB - Last synced: 2 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 0
lcsrodriguez/ENSIIE_S2_PROJET_PROG_FONC
Git repository containing all the resources related to a school project on DNA/RNA strands construction Phylogenetic tree simulation using Functionnal Programming
Language: OCaml - Size: 575 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
zhongyiwang1/Ribo-seq
Pipeline and scripts for the comparative analysis of ribosome profiling and matched RNA sequencing data between organs and across species.
Language: R - Size: 65.3 MB - Last synced: 11 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1
bissessk/RNA-seq-Analysis-of-Control-and-NRDE2-depleted-Breast-Cancer-Cells
Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.
Language: Shell - Size: 418 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
jacobwindsor/SQANTIExplorer
Inter-sample analysis of SQANTI classifications
Language: R - Size: 4.85 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
nadernamini/RNA-seq_Read-algn
RNA-Sequencing Read-Alignment
Language: Jupyter Notebook - Size: 6.32 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
