MultiQC
awesome-single-cell
MultiQC | awesome-single-cell | |
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5 | 3 | |
1,173 | 2,918 | |
1.5% | - | |
9.7 | 5.2 | |
4 days ago | about 1 month ago | |
JavaScript | ||
GNU General Public License v3.0 only | MIT License |
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MultiQC
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R pipelines for bulk RNA-seq analyses
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.
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RNA-seq analysis
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).
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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.
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
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How can I keep Docker MultiQC from ignoring my large files?
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.
awesome-single-cell
- Staying up to date with processes/technology.
- Ex Python users who switched to 100% R (or almost)
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Guidance regarding bulk and scRNA seq analysis.
That may be useful: https://github.com/seandavi/awesome-single-cell
What are some alternatives?
finviz - Unofficial API for finviz.com
cellsnp-lite - Efficient genotyping bi-allelic SNPs on single cells
Sooty - The SOC Analysts all-in-one CLI tool to automate and speed up workflow.
Baltica - Baltica: integrated differential junction usage
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
Awesome-Bioinformatics - A curated list of awesome Bioinformatics libraries and software.
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
scDblFinder - Methods for detecting doublets in single-cell sequencing data
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
DGE_workshop
Sniffles - Structural variation caller using third generation sequencing
clinker - Gene cluster comparison figure generator