Projects in Awesome Lists tagged with transcriptome-assembly
A curated list of projects in awesome lists tagged with transcriptome-assembly .
https://github.com/ablab/spades
SPAdes Genome Assembler
genome-assembly illumina metagenome-assembly next-generation-sequencing sequence-assembler sequencing transcriptome-assembly
Last synced: 05 May 2025
https://github.com/bcgsc/transabyss
de novo assembly of RNA-seq data using ABySS
bioinformatics rna-seq transcriptome transcriptome-assembly
Last synced: 07 May 2025
https://github.com/bcgsc/chopstitch
Finding putative exons and constructing splicegraphs using Trans-ABySS contigs
bloom-filter exon putative-exons splice splice-graphs transcriptome-assembly
Last synced: 07 May 2025
https://github.com/dn070017/quanteval
QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.
connected-components quantification-evaluation-methods transcriptome-assembly
Last synced: 10 Apr 2025
https://github.com/zyxue/vr2c
Visualize read-to-contig alignment during assembly analysis
alignment contig-coverage contigs genome-assembly read-to-contig-alignment transcriptome-assembly
Last synced: 30 Mar 2025
https://github.com/zyxue/kleat
Cleavage site prediction via de novo assembly
alternative-polyadenylation cleavage-sites de-novo-assembly rna-seq transcriptome-assembly
Last synced: 07 Apr 2025
https://github.com/sivkri/rna-seq-scaledlengthtpm
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.
gene-expression genomics genomics-analysis rna-seq rna-seq-analysis rnaseq tpm transcriptome-assembly transcripts-per-million
Last synced: 22 Mar 2025
https://github.com/gauravcodepro/transdecoder-visualization
a regular expression based trinity assembly transdecoder predictions encoder which will parse and will prepare the transcript annotations for visualization with any genome visualization kit such as pygenomeviz, mauve and others, it prepares the coordinates as tuples
geneprediction genome-annotation transcriptome-analysis transcriptome-annotation transcriptome-assembly transcriptome-wide trinity
Last synced: 22 Feb 2025
https://github.com/ibchgenomic/trinity-analyzer
from trinity assembly to deep learning
genome-analysis genome-annotation transcriptome-annotation transcriptome-assembly trinity
Last synced: 18 Mar 2025
https://github.com/applicativesystem/trinity-analyzer
from trinity assembly to deep learning
genome-analysis genome-annotation transcriptome-annotation transcriptome-assembly trinity
Last synced: 16 Dec 2024
https://github.com/gauravcodepro/trinity-blast-machine-learning
a scalable and faster implementation for the genome and the transcriptome annotations for large scale sequencing datasets.
bacterial-genome-analysis bacterial-genomes genome-annotation genome-assembly plantgenomes plantgenomics transcriptome-annotation transcriptome-assembly transcriptome-profiling-data transcriptome-wide transcriptomics trinity
Last synced: 22 Feb 2025
https://github.com/gauravcodepro/tair-gff-ids
A set of functions which will provide easy access and cleaned gff from tair and uses a dataframe and datascience approach to get the systematic tair ids and their coordinates from the tair 10 gff version. It can be applied to any version of the tair for getting the systematic retrival of the tair ids.
genome genome-analysis genome-annotation genome-assembly genome-sequencing tair tair3 transcriptome-annotation transcriptome-assembly
Last synced: 22 Feb 2025