MultiQC
clinker
MultiQC | clinker | |
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5 | 2 | |
1,173 | 501 | |
1.5% | - | |
9.7 | 3.2 | |
4 days ago | 10 months ago | |
JavaScript | Python | |
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.
clinker
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Need help with protein gene-neighborhood methods.
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
What are some alternatives?
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.