Software
A public repository for many of our tools and scripts can be found on Github.
| hpgltools | a collection of R functions to aid in host-pathogen genomic research |
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| gene-structure-analysis | visualization and descriptive statistics of Trypanosome gene structure using RNA-Seq data |
| eupathdb-organismdb | scripts to help automate the process of generator Bioconductor OrgDb, TranscriptDb, and OrganismDb packages for species hosted on EuPathDB |
| ptu-detection | a simple script for detecting polycistronic transcriptional units (PTUs) in trypanosomatid genomes |
| utr_analysis | pipeline for determining the 5'UTR spliced leader and 3'UTR poly-A acceptor sites in a collection of RNA-Seq reads |
Recent Datasets
We are committed to public data release. Please let us know if there is anything you can't find.
Note: TriTryp Genome sequences and annotations are maintained and curated at TriTrypDB.
| Meta-transcriptome profiling of the human-Leishmania braziliensis cutaneous lesion. | Sequence data in SRA under Bioproject PRJNA307599. Accession numbers for individual Biosamples are provided in Table S1 of this paper. |
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| Transcriptome Profiling of Human Foreskin Fibroblasts Infected with T. cruzi Sylvio Strain of Trypanosoma cruzi. | Sequence data in SRA under Bioprojects PRJNA251582 (human reads) and PRJNA251583 (parasite reads). Accession numbers for individual Biosamples are provided in Table S1 of this paper. |
| Dual transcriptome profiling of Leishmania-infected human macrophages. | Sequence data in SRA under Bioprojects PRJNA290995 (human), PRJNA252769 (L. major), and PRJNA292915 (L. amazonensis). Accession numbers for individual Biosamples are provided in Table S1 of this paper. |
| Transcriptome remodeling in Trypanosoma cruzi and human cells during intracellular infection. | Sequence data in SRA under Bioproject PRJNA251582 with accession numbers SRR1346026-SRR1346052 (for uninfected and infected HFFs) and Bioproject PRJNA251583 with accession numbers SRR1346053-SRR1346059 (for data from T. cruzi extracellular forms). Accessions for individual Biosamples are provided in Table S1 of this paper. |
| Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell. | Sequence data in SRA under Bioproject PRJNA252791 with accession numbers SRR1460724-SRR1460747 (for uninfected and infected macrophages), PRJNA252769 (for data from L. major extracellular forms) with accession numbers SRR1460767, SRR1460772, and SRR2136702. Accessions for individual Biosamples are provided in Table S1 of this paper. |
| Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation. | Sequence data in SRA under Bioproject PRJNA252769 with accession numbers SRR1460763-SRR1460775. Accessions for individual Biosamples are provided in Table S1 of this paper. |
| The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling. | Sequence data in SRA under Bioproject PRJNA273778 with accession numbers SRR1918864, SRR1918994, SRR1918999-SRR1919012, and SRR1919014-SRR1919018. Accessions for individual Biosamples are provided in Supplemental Table 2 of this paper. |