elsayed-lab

hpgltools

A collection of R functions to aid in host-pathogen genomic research

utr_analysis

Pipeline for determining the 5'UTR spliced leader and 3'UTR poly-A acceptor sites in a collection of RNA-Seq reads

dantools

Utilities to compare disparate genomes

manuscript-shared-rnaseq

R and Rmarkdown code used across multiple RNA-Seq projects.

CYOA

CL_biopsies_Colombia

container recipe to perform analyses examining cutaneous leishmania biopsies with CIDEIM published approximately 202310

clinical_strains_analyses

coex-network-optimization-construction

Code for submitting co-expression network construction jobs to a cluster and summarizing the results

fe_adipocyte_analyses

fetch-eupathdb-resources

Shell script to retrieve specific resources (FASTA, GFF, etc.) from TriTrypDB for a given set of species

gene-structure-analysis

Visualization and descriptive statistics of Trypanosome gene structure using RNA-Seq data.

gene-structure-determination

Gene structure determination and novel ORF detection using RNA-Seq data

hpgltools_singularity

macrophage_response_lpanamensis

singularity container comprising analyses of macrophages infected with Leishmania panamensis.

manuscript-coex-networks

Functional enrichment analysis of individual and ensemble co-expression networks

ptu-detection

A simple script for detecting polycistronic transcriptional units (PTUs) in Trypanosomatid genomes.

rnaseq_kajal_2020

tmrc_metabolome

Some shared information from the TMRC metabolomics experiment

tnseq_spyogenes_2017

TNSeq analyses on Streptococcus pyogenes strain 5448 performed in 2017.

tryp-reg-predict

Trypanosomatid Regulatory Element Prediction Pipeline

TxDb.LmajorFriedlin.tritryp32.genes

Transcript annotation package for Leishmania major strain Friedlin

TxDb.TcruziCLBrenerEsmer.tritryp32.genes

Transcript annotation package for T. cruzi strain CL Brener Esmeraldo-like haplotype

utr_length_composition_and_site_usage_analysis

UTR Length, Composition, and Alternative Trans-splicing / Poly-adenylation Analysis

clinical_strains_lpanamensis

singularity container comprising the comparison of some clinical strains

cure_fail_host_analyses

Container recipe for repeating the L.panamensis cure/fail analyses in the host.

lmajor_alternate_acceptor_site_usage

Analysis comparing the use of alternative trans-splicing and alternative-polyadenylation sites across developmental stages in Leishmania major

org.TcCLB.esmer.tritryp.db

Genome wide annotations for Trypanosoma cruzi strain Friedlin Esmeraldo-like

spirogyra_assembly

A relatively minimal de-novo algal RNA assembly.