Package for fetching metadata and downloading data from SRA/ENA/GEO
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Oct 25, 2024 - Python
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sratoolkit
Here are 12 public repositories matching this topic...
GEO RNA-seq Experiments Processing Pipeline
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Oct 25, 2019 - R
dockerfile
bioinformatics
r
docker-image
fair
bioinformatics-data
bioinformatics-databases
sra-files
rpackage
sratoolkit
bioinformatics-tool
dbgap
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Jul 26, 2019 - Jupyter Notebook
fast utils for fetch and dump NCBI SRA archive raw data
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May 25, 2023 - Python
A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.
shell
bash
cli
r
ubuntu
nextflow
hpc
deseq2
google-cloud-platform
samtools
featurecounts
bowtie
ngs-analysis
cutadapt
ngs-pipeline
fastqc
sratoolkit
apptainer
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Nov 21, 2024 - Nextflow
Download Raw Reads from SRA Archive
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Feb 8, 2018 - Nextflow
Decrypt the encrypted genome data files using SRA Toolkit
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Apr 6, 2019
RNA-seq code with Bowtie alignment and generating strain-specific counts using Emase
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Apr 4, 2022 - HTML
PARMIK is a fast and memory-efficient tool for identifying the "Partial Match" region between two genomic sequences.
smith-waterman
k-mer
k-mer-frequency
k-mer-hashing
genome-analysis
bwa-mem
metagenomic-analysis
blastn
sratoolkit
genome-alignment
dna-processing
environment-sampling
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Oct 18, 2024 - C++
RNA-seq analysis from FASTQ to differential gene-expression using open-source tools
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Nov 19, 2024 - Jupyter Notebook
explore sra databases and sequence retrieval
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Aug 17, 2024 - Shell
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