To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.
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Updated
Jun 9, 2023 - R
To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.
a_inornata research project
Bioinformatics Programming - Transcriptome Assembly
Cleavage site prediction via de novo assembly
an investigation into the efficiency of Trinity transcriptome assemblies
transdecoder predictions analyzer for pygenomeviz, mauve.
Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"
Assembler for multiple RNA-seq samples
from trinity assembly to deep learning.
ease of access gff files from tair for reading tair ids.
A pipeline for the assembly of VAR genes from transcriptome data
Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.
Visualize read-to-contig alignment during assembly analysis
MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing
A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity
The AugusMake pipeline is a Snakemake-based workflow for generating gene annotations using the Augustus software. AugusMake can perform gene predictions using any combination of the three methods: ab initio, with extrinsic hints, or by training a new species.
Biocore's de novo transcriptome assembly workflow based on Nextflow
tool for long read transcriptome assembly
These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline
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