MultiQC vs clinker

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MultiQC		clinker
	Project
5	Mentions	2
1,173	Stars	501
1.5%	Growth	-
9.7	Activity	3.2
4 days ago	Latest Commit	10 months ago
JavaScript	Language	Python
GNU General Public License v3.0 only	License	MIT License

The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.

MultiQC

Posts with mentions or reviews of MultiQC. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-12-09.

R pipelines for bulk RNA-seq analyses
3 projects | /r/bioinformatics | 9 Dec 2023

fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.
RNA-seq analysis
1 project | /r/bioinformatics | 16 Nov 2022

I would recommend looking at the pages for FastQC and MultiQC. I run FastQC on my fastq files, then MultiQC on them to collect all that individual data into one report. You can also use MultiQC to analyze the quality of your alignments, at least after using STAR aligner (probably others too, I just have only used STAR aligned).
How to use MultiQC? I am trying to run it to compile the summary from my FASTQC but I keep getting the "Sample has no read" error.
2 projects | /r/bioinformatics | 18 Aug 2021

If that all checks out then I would have to see more of your files in order to help, sorry. Submitting the issue at https://github.com/ewels/MultiQC/issues would help you more
How can I keep Docker MultiQC from ignoring my large files?
1 project | /r/bioinformatics | 17 Aug 2021

I have seen this Github thread, but it is not applicable for me because I am not running MultiQC natively, I am running a docker version of it in HPC.

clinker

Posts with mentions or reviews of clinker. We have used some of these posts to build our list of alternatives and similar projects.

Need help with protein gene-neighborhood methods.
1 project | /r/bioinformatics | 15 Aug 2021

Being a silent reader all this while, this is my first question here and a very basic indeed. I want to generate some gene neighborhood clusters for a set of protein fasta files I have from UniProtKB. I plan to use: 1. http://www.webflags.se/ and 2. https://github.com/gamcil/clinker
Stuck Running Bioinformatics Tool Through Command
1 project | /r/bash | 21 Dec 2020

What are some alternatives?

When comparing MultiQC and clinker you can also consider the following projects:

finviz - Unofficial API for finviz.com

ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers

Sooty - The SOC Analysts all-in-one CLI tool to automate and speed up workflow.

pyCirclize - Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

awesome-single-cell - Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

quast - Genome assembly evaluation tool

tm_calculator_gui - Calculates the melting temperature(in Celsius) of a user imported forward and reverse primer based on primer blast default parameters & pcr additives

pyGenomeViz - A genome visualization python package for comparative genomics

pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

dash - Data Apps & Dashboards for Python. No JavaScript Required.

Osintgram - Osintgram is a OSINT tool on Instagram. It offers an interactive shell to perform analysis on Instagram account of any users by its nickname

scanpy - Single-cell analysis in Python. Scales to >1M cells.