OliveiraDS-hub

PhD candidate interested in bioinformatics analyses to understand how TEs can promote genomic variability in nature.

Université Claude Bernard Lyon 1Lyon

Pinned Repositories

ChimeraTE
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
Language:Python20 1 216
drosophila-transposons
Drosophila transposable element canonical sequences
Language:Rich Text Format00
EDTA
Extensive de-novo TE Annotator
Language:Perl00
FasTE
A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotator (EDTA), DeepTE, RepeatMasker and RM_TRIPS.
Language:R00
hyphy
HyPhy: Hypothesis testing using Phylogenies
Language:HyPhy00
motility
Language:Prolog00
rosette_tetools
Rosette files required to run TEtools pipeline
00
SQuIRE
Software for Quantifying Interspersed Repeat Expression
Language:Python0 0 00
telescope
Quantification of transposable element expression using RNA-seq
Language:Python00
TEs_expression_commandline
Command line used in "Oxidative and radiation stress induce transposable elements transcription in Drosophila melanogaster" study.
Language:R10

OliveiraDS-hub/ChimeraTE
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
Language:Python20 1 216
OliveiraDS-hub/TEs_expression_commandline
Command line used in "Oxidative and radiation stress induce transposable elements transcription in Drosophila melanogaster" study.
Language:R10
OliveiraDS-hub/drosophila-transposons
Drosophila transposable element canonical sequences
Language:Rich Text Format00
OliveiraDS-hub/EDTA
Extensive de-novo TE Annotator
Language:Perl00
OliveiraDS-hub/FasTE
A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotator (EDTA), DeepTE, RepeatMasker and RM_TRIPS.
Language:R00
OliveiraDS-hub/hyphy
HyPhy: Hypothesis testing using Phylogenies
Language:HyPhy00
OliveiraDS-hub/motility
Language:Prolog00
OliveiraDS-hub/rosette_tetools
Rosette files required to run TEtools pipeline
00
OliveiraDS-hub/SQuIRE
Software for Quantifying Interspersed Repeat Expression
Language:Python0 0 00
OliveiraDS-hub/telescope
Quantification of transposable element expression using RNA-seq
Language:Python00
OliveiraDS-hub/TuataraTELandscapes
Transposable element landscape figures for the Tuatara genome paper 2020