| Deposited data |
|
| tRFUniverse (source code) |
GitHub |
https://github.com/knowmics-lab/tRFUniverse |
| TCGA (small RNA-Seq) |
NCBI-dbGaP |
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178.v11.p8 |
| TARGET (small RNA-Seq) |
NCBI-dbGaP |
https://www.cancer.gov/ccg/research/genome-sequencing/target/using-target-data/citing |
| NCI-60 (PRJNA390643) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA390643 |
| Biological fluids (PRJNA242348) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA242348 |
| Biological fluids (PRJNA415462) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA415462 |
| Biological fluids (PRJNA431173) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA431173 |
| Biological fluids (PRJNA445720) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA445720 |
| Biological fluids (PRJNA505788) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA505788 |
| Biological fluids (PRJNA527257) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA527257 |
| Biological fluids (PRJNA647356) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA647356 |
| AGO CLASH/CLEAR-Seq data (PRJNA217521) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA217521 |
| AGO CLASH/CLEAR-Seq data (PRJNA691465) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA691465 |
| AGO CLASH/CLEAR-Seq data (PRJNA296130) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA296130 |
| AGO CLIP-Seq data (PRJNA129395) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA129395 |
| AGO CLIP-Seq data (PRJNA176418) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA176418 |
| AGO CLIP-Seq data (PRJNA248264) |
NCBI-SRA |
https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA248264 |
|
| Software and algorithms |
|
| Samtools (v.1.12) |
Ubuntu package |
https://manpages.ubuntu.com/manpages/jammy/man1/samtools.1.html |
| Trim Galore (v.0.6.6) |
The Babraham Institute |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| Bowtie 2 (v.2.4.5) |
Bioconda |
https://anaconda.org/bioconda/bowtie2 |
| tRFexplorer (data) |
GitHub |
https://github.com/knowmics-lab/tRFexplorer |
| MINTmap (v.2) |
Jefferson |
https://cm.jefferson.edu/mintmap/ |
| Bedtools (v.2.30.0) |
Bioconda |
https://anaconda.org/bioconda/bedtools |
| Flexbar (v.2.5) |
Ubuntu package |
https://manpages.ubuntu.com/manpages/jammy/man1/flexbar.1.html |
| CLASH Analyst |
GitHub |
https://github.com/t50504/CLASHanalyst |
| RNAhybrid |
Ubuntu package |
https://manpages.ubuntu.com/manpages/trusty/man1/RNAhybrid.1.html |
| MACS2 (v.2.2.7.1) |
PyPI |
https://pypi.org/project/MACS2/ |
| Laravel (v.9.19) |
Composer |
https://packagist.org/packages/laravel/framework |
| Next.js (v.12.2.5) |
NPM |
https://www.npmjs.com/package/next |
| JBrowse 2 (v.2.1.5) |
NPM |
https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| R (v.4.2) |
Ubuntu package |
https://cloud.r-project.org/ |
