duartebred/Analise-RNASeq-Cancro-Utero

Repositório para apresentação de código, datasets e posterior análise, desenvolvido pelo grupo 5 para a UC Extração de Conhecimento de Dados Biológicos, do Mestraddo em Bioinformática, ano lectivo 23-24.

Language: HTML - Size: 34.2 MB - Last synced: about 8 hours ago - Pushed: about 14 hours ago - Stars: 0 - Forks: 0

datirium/workflows

CWL based Bioinformatics Workflows

Language: Common Workflow Language - Size: 2.86 MB - Last synced: about 3 hours ago - Pushed: about 15 hours ago - Stars: 14 - Forks: 13

HorvathLab/NGS

Next-Gen Sequencing tools from the Horvath Lab

Language: Python - Size: 145 MB - Last synced: about 14 hours ago - Pushed: about 17 hours ago - Stars: 37 - Forks: 15

LieberInstitute/Habenula_Pilot

habenulaPilot project code repository

Language: HTML - Size: 2.75 GB - Last synced: about 15 hours ago - Pushed: about 18 hours ago - Stars: 0 - Forks: 0

gagneurlab/drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Language: Python - Size: 110 MB - Last synced: about 18 hours ago - Pushed: about 22 hours ago - Stars: 127 - Forks: 42

GuyTeichman/RNAlysis

RNA sequencing analysis software

Language: Python - Size: 613 MB - Last synced: about 7 hours ago - Pushed: about 20 hours ago - Stars: 121 - Forks: 13

huangyh09/brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

Language: Python - Size: 1.72 MB - Last synced: about 11 hours ago - Pushed: 1 day ago - Stars: 40 - Forks: 15

HHHit/DL-based-Tumor-Classification

Deep Learning Based Tumor Type Classification Using Gene Expression Data

Language: Python - Size: 16.4 MB - Last synced: about 13 hours ago - Pushed: 1 day ago - Stars: 21 - Forks: 16

Melclic/intersectomics

Package to study time series (or other series) multi-omics patterns of expresssion with replicates

Language: Python - Size: 1.52 MB - Last synced: about 14 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

ablab/IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Language: Python - Size: 18.7 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 120 - Forks: 11

bigomics/omicsplayground

Visual self-service analytics platform for big omics data.

Language: R - Size: 1.15 GB - Last synced: about 18 hours ago - Pushed: about 18 hours ago - Stars: 114 - Forks: 34

sebastian-gregoricchio/Rseb

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

Language: R - Size: 12.9 MB - Last synced: about 20 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 1

ScienceComputing/NGSOmics_Programming

Computational biology/bioinformatics workflows, codes, and concept notes on NGS data

Language: HTML - Size: 8.07 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 5 - Forks: 0

royfrancis/rskb

Guide and links related to bulk and single-cell RNA-Seq experiments.

Language: TeX - Size: 19.5 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

nf-core/rnafusion

RNA-seq analysis pipeline for detection of gene-fusions

Language: Nextflow - Size: 18.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 130 - Forks: 89

ccb-hms/osca-workbench

Single-cell RNAseq materials derived from the 2023 ISMB OSCA workshop in the carpentries workbench format.

Language: R - Size: 879 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

carpentries-incubator/rna-seq-data-for-ml

RNA-Seq: Data Readiness for Machine Learning Applications

Language: R - Size: 47.5 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 2 - Forks: 3

bcgsc/RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads

Language: Java - Size: 2.41 MB - Last synced: 2 days ago - Pushed: 4 months ago - Stars: 82 - Forks: 7

lpantano/DEGreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Language: R - Size: 51.7 MB - Last synced: 2 days ago - Pushed: 3 months ago - Stars: 22 - Forks: 16

popitsch/rnalib

rnalib: a python-based transcriptomics library

Language: Jupyter Notebook - Size: 327 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

gagneurlab/FRASER Fork of c-mertes/FRASER

Language: R - Size: 14.3 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 13 - Forks: 4

nf-core/rnaseq

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

Language: Nextflow - Size: 64.1 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 787 - Forks: 653

Center-for-Health-Data-Science/bulkDGD

Code, documentation, and tutorial for the DGD model trained on bulk RNA-Seq data.

Language: Python - Size: 24.6 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 7 - Forks: 3

zerostwo/rna-seq

A Snakemake workflow for RNA-seq analysis

Language: Python - Size: 5.86 KB - Last synced: 4 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

biocorecrg/MOP2

Master of Pores 2

Language: Nextflow - Size: 209 MB - Last synced: 2 days ago - Pushed: 6 months ago - Stars: 22 - Forks: 7

getzlab/rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

Language: C++ - Size: 12.7 MB - Last synced: 4 days ago - Pushed: 25 days ago - Stars: 140 - Forks: 19

senzhaocode/FuSViz

A web app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples.

Language: JavaScript - Size: 78.9 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 5 - Forks: 4

galantelab/freddie

Tool to identify chimeric events from RNA-Seq data

Language: Shell - Size: 22.8 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 2 - Forks: 0

SaraAghamiri/Radiogenomics_tutorial0

The purpose of this GitHub repository is to provide a prototype for conducting radiogenomics research, particularly focusing on the interplay between imaging features and genomic profiles in glioblastoma patients.

Language: Jupyter Notebook - Size: 346 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 3 - Forks: 1

t-neumann/slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity

Language: Python - Size: 39.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 36 - Forks: 22

montilab/pipeliner

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Language: Nextflow - Size: 23.2 MB - Last synced: 5 days ago - Pushed: over 4 years ago - Stars: 43 - Forks: 14

c-mertes/FRASER

FRASER - Find RAre Splicing Events in RNA-seq

Language: R - Size: 14.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 30 - Forks: 19

deeptools/deepTools

Tools to process and analyze deep sequencing data.

Language: Python - Size: 118 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 645 - Forks: 205

nf-core/differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Language: Nextflow - Size: 7.77 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 45 - Forks: 24

Kuanhao-Chao/splam-analysis-results

all the scripts to reproduce the results in the splam paper

Language: Python - Size: 1.04 GB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 0

snowGlint/easybio

an interface for common bioinformatics analyses

Language: R - Size: 3.53 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0

PavlidisLab/rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Language: Python - Size: 43.5 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 19 - Forks: 4

pachterlab/GPCTP_2019-2

Size: 1000 Bytes - Last synced: 6 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 1

pachterlab/kallisto

Near-optimal RNA-Seq quantification

Language: C - Size: 9.27 MB - Last synced: 6 days ago - Pushed: 10 days ago - Stars: 623 - Forks: 169

UBrau/ProcessDE

Processing RNAseq data for gene expression analysis

Language: R - Size: 30.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

almeidasilvaf/plant_transcriptomes

Data and code used in the Plant Genomes dashboard

Language: R - Size: 1.72 MB - Last synced: 7 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

gagneurlab/FRASER-analysis

Accompanying analysis code for the FRASER manuscript

Language: R - Size: 4.67 MB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 23 - Forks: 7

nf-core/rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Language: Nextflow - Size: 160 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 33 - Forks: 21

rnabioco/rhumba

Snakemake pipelines for RNA sequencing data

Language: C - Size: 21.2 MB - Last synced: 7 days ago - Pushed: 11 months ago - Stars: 2 - Forks: 2

pachterlab/sleuth

Differential analysis of RNA-Seq

Language: R - Size: 33.1 MB - Last synced: 6 days ago - Pushed: 11 months ago - Stars: 300 - Forks: 96

rnabioco/scRNA-seq-Cell-Ref-Matrix

A reference matrix atlas of all single cell RNA-seq data on NCBI GEO for mice and humans

Language: R - Size: 338 MB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 4 - Forks: 1

foerstner-lab/READemption

A pipeline for the computational evaluation of RNA-Seq data

Language: Python - Size: 295 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 35 - Forks: 19

crazyhottommy/RNA-seq-analysis

RNAseq analysis notes from Ming Tang

Language: Python - Size: 548 KB - Last synced: 7 days ago - Pushed: over 2 years ago - Stars: 840 - Forks: 290

FEI38750/MTD

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data

Language: R - Size: 23.7 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 14 - Forks: 7

nanoporetech/pychopper 📦

A tool to identify, orient, trim and rescue full length cDNA reads

Language: Python - Size: 52 MB - Last synced: 7 days ago - Pushed: almost 2 years ago - Stars: 78 - Forks: 22

earmingol/cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Language: Python - Size: 97.8 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 51 - Forks: 11

BgeeDB/bgee_pipeline

Source code of the Bgee pipeline used to build the Bgee database

Language: Perl - Size: 1020 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 11 - Forks: 4

hms-dbmi/dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

Language: R - Size: 34.3 MB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 19 - Forks: 4

zitunstu24/rnaseq-mapper-species-py

This python tool is for downloading and mapping RNA-Seq data from NCBI for different species

Language: Python - Size: 4.88 KB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

sib-swiss/single-cell-training

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Language: R - Size: 211 MB - Last synced: 4 days ago - Pushed: about 2 months ago - Stars: 69 - Forks: 31

nf-core/spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Language: Nextflow - Size: 6.94 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 39 - Forks: 12

Kuanhao-Chao/splam

✂️ Deep learning-based splice site predictor that improves spliced alignments

Language: C++ - Size: 1.22 GB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 28 - Forks: 1

MViscardi-UCSC/nanoporePipelineScripts

Marcus Viscardi's personal scripts used to analyze outputs of dRNA seq w/ ONT. Please feel free to reach out if you are interested in utilizing any of this code!

Language: Jupyter Notebook - Size: 121 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 1 - Forks: 0

harrlol/hamrbox

A bundle of HAMRtools for High-throughput RNA modification prediction and analysis

Language: R - Size: 111 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 1

velocyto-team/velocyto.py

RNA velocity estimation in Python

Language: Python - Size: 9.83 MB - Last synced: 9 days ago - Pushed: 9 months ago - Stars: 153 - Forks: 82

kkwock/VARify

Transcriptional variant verification to validate predicted variants from genomic data in expressed transcripts

Language: HTML - Size: 48.9 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

pathint/RankCompV3.jl

RankCompV3: a differential expression analysis algorithm based on the relative expression orderings (REOs) of gene pairs

Language: Julia - Size: 9.39 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 5 - Forks: 0

NerdVerse2024/Milk_metagenomics

Milk Metagenomics Analysis of Cow Milk Samples across Global sites Using Mothur

Size: 147 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

kevinhu/mdm4-splicing

Computational analysis of RPL22 alterations and impact on MDM4 splicing

Language: Jupyter Notebook - Size: 938 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

Drapythron/SARS-CoV-2-Challenge

Language: Python - Size: 3.25 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 0

rohan-b-84/dge_analysis_using_DESeq2

Differential Gene Expression analysis in R using DESeq2

Language: HTML - Size: 2.53 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

mckellardw/ref_snake

Snakemake workflow to automatically build and organize reference genomes for common alignment tasks

Language: JavaScript - Size: 3.4 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 2 - Forks: 1

jsa-aerial/aerobio

Extensible full DAG streaming computation server with services and jobs for RNA-Seq, Tn-Seq, WG-Seq and Term-Seq.

Language: Clojure - Size: 920 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 8 - Forks: 1

cenk-celik/kaliya_perumal_d_rerio

RNA-seq analysis for zebrafish with muscle injury

Language: R - Size: 40 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

bicciatolab/popsicleR

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.

Language: R - Size: 48.3 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 24 - Forks: 7

federicomarini/HCAData

Access data from the Human Cell Atlas project, directly via R/Bioconductor

Language: R - Size: 7.37 MB - Last synced: 6 days ago - Pushed: 14 days ago - Stars: 8 - Forks: 2

federicomarini/ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Language: R - Size: 24 MB - Last synced: 6 days ago - Pushed: 14 days ago - Stars: 29 - Forks: 7

ytakemon/1415-Col4a5xDO-Project

Scripts used for the 1415 Col4a5xDO project

Language: HTML - Size: 31.9 MB - Last synced: 14 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

YogiOnBioinformatics/Teaching-Assistant-Computational-Genomics

Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.

Language: Shell - Size: 809 KB - Last synced: 14 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

y9c/cutseq

✂️ Trim sequencing adapters from NGS data automatically

Language: Python - Size: 2.89 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 3 - Forks: 0

COMBINE-lab/alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Language: Rust - Size: 4.08 MB - Last synced: 7 days ago - Pushed: 2 months ago - Stars: 152 - Forks: 15

swsoyee/Nucleotide-sequence-analysis-by-R

👨‍🎓(Rで)塩基配列解析

Language: R - Size: 960 KB - Last synced: 15 days ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

guma44/GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

Language: Jupyter Notebook - Size: 13.3 MB - Last synced: 2 days ago - Pushed: 23 days ago - Stars: 130 - Forks: 49

KevinMenden/scaden

Deep Learning based cell composition analysis with Scaden.

Language: Python - Size: 1.08 MB - Last synced: 13 days ago - Pushed: almost 3 years ago - Stars: 68 - Forks: 24

dtm2451/dittoSeq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Language: R - Size: 18.7 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 167 - Forks: 17

hayeonrjoe/RNA-seq

Record of my RNA sequencing analyses

Language: Jupyter Notebook - Size: 97.8 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

lbcb-sci/RiNALMo

RiboNucleic Acid (RNA) Language Model

Language: Python - Size: 326 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 21 - Forks: 3

insightsengineering/hermes

Preprocessing, analyzing, and reporting of RNA-seq data

Language: R - Size: 45.2 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 11 - Forks: 2

agitter/single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Size: 244 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 384 - Forks: 58

ibenjame/SM-PATseq

Snakemake workflow for SM-PATseq

Language: R - Size: 39.1 KB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

danilotat/UTR_add_extend_GTF

Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.

Language: Python - Size: 34.2 KB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 5 - Forks: 2

swsoyee/TCC-GUI

📊 Graphical User Interface for TCC package

Language: R - Size: 37.7 MB - Last synced: 15 days ago - Pushed: 2 months ago - Stars: 43 - Forks: 18

PengBingming/idbview

A database and interactive platform for respiratory-associated disease.

Language: R - Size: 82 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

pachterlab/kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Size: 124 MB - Last synced: 6 days ago - Pushed: almost 2 years ago - Stars: 110 - Forks: 30

hamidghaedi/Enrichment-Analysis

From RNA-seq raw reads to enriched pathways by DEGs

Size: 719 KB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 28 - Forks: 14

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.6 MB - Last synced: 16 days ago - Pushed: 20 days ago - Stars: 17 - Forks: 6

saeyslab/nichenetr

NicheNet: predict active ligand-target links between interacting cells

Language: R - Size: 151 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 437 - Forks: 113

davetang/rnaseq

RNA-seq analyses.

Language: Shell - Size: 5.13 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 6 - Forks: 5

snakemake-workflows/rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Language: Python - Size: 5.39 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 63 - Forks: 41

poseidonchan/TAPE

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Language: Jupyter Notebook - Size: 161 MB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 42 - Forks: 10

bpucker/teaching

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Size: 268 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 40 - Forks: 8

kanaverse/kana

Single cell analysis in the browser

Language: JavaScript - Size: 128 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 131 - Forks: 12

slipnitskaya/regulAS

regulAS: A Bioinformatics Tool for the Integrative Analysis of Alternative Splicing Regulome using RNA-Seq data

Language: Python - Size: 609 KB - Last synced: 6 days ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

anergictcell/Wigfiles

Language: Ruby - Size: 1.05 MB - Last synced: 22 days ago - Pushed: about 7 years ago - Stars: 0 - Forks: 1

bixBeta/nextflow

nextflow RNAseq pipeline for GG02

Language: Nextflow - Size: 1.14 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0