RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. (by nf-core)

Rnaseq Alternatives

Similar projects and alternatives to rnaseq

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a better rnaseq alternative or higher similarity.

rnaseq reviews and mentions

Posts with mentions or reviews of rnaseq. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-09-07.
  • Generate GUIs and deploy bioinformatics workflows with python
    3 projects | reddit.com/r/bioinformatics | 7 Sep 2022
    First lets recognize that the framework presented has new features that don't exist in the previous DSLs you mention. Many developers highly value these additions and they along could justify a new stab at a workflow language: and for many the represent tradeoff * Interface generation * Declarative cloud resource provisionment * Static typing * Native python support This workflow has a similar level of complexity to nf-core/rnaseq (not the same, but similar in number of constituent tasks for the purpose of counting transcript abundance). It ingests raw sequencing reads, runs QC + trimming, does psuedo-alignment, recovers counts from abundance estimates, and aggregates counts over a many samples for direct use by diff-exp tools. (It is not 'running salmon'. I think that is a reductionist take.) It does this in addition to dynamically building React.js interfaces, adding static type validation to input parameters, and deploying cloud infrastructure in a simpler way. For the lines of code comparison, I think it is a weird way to compare software as the number of lines of code is no proxy for legibility, ease of development, likelihood of long-term maintenance (many more people know python than nextflow). Nonetheless nf-core/rnaseq has nearly 1000 lines alone in its workflow entrypoint alone - https://github.com/nf-core/rnaseq/blob/master/workflows/rnaseq.nf . With imported modules + subworkflows, LOC actually reaches the many thousands.. (Now I understand it is more complex and mature, but I highlight why I think the comparison is weird and wonder what you are even comparing to.) Whereas the entire logic of the presented pipeline is actually neatly encapsulated in 1200 lines of a single file. Overall this feels like a that doesn't come from a place of rational discourse, rather group dislike for something new and different. What I would like to do is address and talk about specific technical points (preferably over issues on github) so conversations can be productive and improve the tools I am working on.
  • I've been really frustrated with picking the right tools for bulk RNA-seq, so I did a long literature review and wrote this workflow
    3 projects | reddit.com/r/bioinformatics | 4 Aug 2022
  • Software repository and hackathons
    6 projects | reddit.com/r/longevity | 29 Jun 2022
  • Introduction to RNAseq and microRNA?
    2 projects | reddit.com/r/bioinformatics | 23 Feb 2022
  • Tkinter for python 3.10 broken on MacOS?
    2 projects | reddit.com/r/Python | 7 Oct 2021
    Not really sure why it's a problem for you, I'm working on rnaseq and they use a very big input dataset, also outputs huge datasets too. It uses docker so you can deploy fast on VMs.
  • A note from our sponsor - InfluxDB
    www.influxdata.com | 2 Feb 2023
    InfluxDB is the Time Series Platform where developers build real-time applications for analytics, IoT and cloud-native services. Easy to start, it is available in the cloud or on-premises. Learn more →


Basic rnaseq repo stats
1 day ago

nf-core/rnaseq is an open source project licensed under MIT License which is an OSI approved license.

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