104 Open source projects that are alternatives of or similar to pipeline-pinfish-analysis

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

Reference-based transcript discovery from long RNA read

A versatile sequenced read processor for nanopore direct RNA sequencing

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

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

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

RNASeq pipeline

CellNet: network biology applied to stem cell engineering

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

scRNA-seq data visualization from scrattch

Dynamical systems methods for RNA velocity analysis

An automated RNA-seq pipeline using Nextflow

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Feature extraction algorithm for genomic data

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

An accurate and ultra-fast hybrid genome assembler

A graphical user interface for distributed data processing of high throughput genomics

Multi-omics analysis protocols by Lyu.

Streamlining SLAM-seq analysis with ultra-high sensitivity

FEELnc : FlExible Extraction of LncRNA

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

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

Genome Annotation Without Nightmares

Porting DESeq2 and DEXSeq into python via rpy2

A fast tool for hybrid genome assembly of long and short reads

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Single cell analysis in the browser

🚦 Run Picard on BAM files and collate 90 metrics into one file.

SARS-CoV-2 workflow for nanopore sequence data

Version 2.1.0 released

📊 Graphical User Interface for TCC package

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

A curated list of awesome nanopore analysis tools.

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Processing of single cell RNAseq data for the recovery of TCRs in python

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Deep Learning based cell composition analysis with Scaden.

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

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

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

Differential Gene Correlation Analysis

RNA-seq analysis pipeline for detection gene-fusions

Fast and accurate gene fusion detection from RNA-Seq data

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

Summer school course materials collection

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

PEPPER-Margin-DeepVariant

Fast in-silico normalization algorithm for NGS data

A pipeline for the computational evaluation of RNA-Seq data

Next-Gen Sequencing tools from the Horvath Lab

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.