The original R code was written by Avi Feller and Jacob Lemieux and is described in this publication:
Lemieux JE, Gomez-Escobar N, Feller A, Carret C, Amambua-Ngwa A, Pinches R, Day F, Kyes SA, Conway DJ, Holmes CC and Newbold CI (2009): Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture. Proc Natl Acad Sci U S A 106(18), 7559-7564 doi: 10.1073/pnas.0811829106 https://www.pnas.org/doi/full/10.1073/pnas.0811829106
In this deposition, the original R script is adapted for command-line use. For usage instructions, see file "README.md".
Furthermore, this deposition contains RNA-seq data for P. falciparum 3D7 cultured with blood from individuals with high, normal or low iron status (experiment 1) or with blood from a healthy donor in the presence vs. absence of 0.7 µM hepcidin (experiment 2) at 6 – 9 and 26 – 29 hours post erythrocyte invasion (hpi). For more details see publication:
Iron transport pathways in the human malaria parasite Plasmodium falciparum revealed by RNA-sequencing, Wunderlich et al. (biorxiv).
Finally, this deposition contains a variety of pre-processed datasets obtained from the following references:
Bártfai R, Hoeijmakers WA, Salcedo-Amaya AM, Smits AH, Janssen-Megens E, Kaan A, Treeck M, Gilberger TW, Françoijs KJ and Stunnenberg HG (2010): H2A.Z demarcates intergenic regions of the Plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3. PLoS Pathog 6(12), e1001223 doi: 10.1371/journal.ppat.1001223
Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL and Sabeti PC (2015): Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics 16(1), 454 doi: 10.1186/s12864-015-1603-4
López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K and Su X-z (2011): Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genomics 12(1), 587 doi: 10.1186/1471-2164-12-587
Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C and Llinás M (2010): New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol 76(1), 12-24 doi: 10.1111/j.1365-2958.2009.07026.x
Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, M...