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CCR Collaborative Bioinformatics Resource

Pipelines & Software

  • Whole Exome and Genome Pipelines
  • Single Cell RNA-Seq Pipeline
  • RNA-Seq Pipelines
  • ChIP-Seq Pipeline

whole exome and genome pipeline overview

Single Cell RNA-Seq Pipeline

RNA-Seq_pipeline overview

Chip-Seq pipeline overview

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Upcoming Classes

  • Single-cell RNA-Seq Analysis on NIDAP – Tutorial & Discussion
  • Bulk RNA-Seq Analysis on NIDAP – Tutorial & Discussion
  • Single-cell RNA-Seq Analysis on NIDAP – Tutorial & Discussion

Recent CCBR Publications

  • 03/01/2020 - An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses
  • 02/01/2020 - Mosaicism for KCNJ5 causing early-onset primary Aldosteronism due to bilateral Adrenacortical Hyperplasia
  • 01/01/2020 - Immunotherapy with DNA vaccine and live attenuated rubella/SIV gag vectors plus early ART can prevent SIVmac251 viral rebound in acutely infected rhesus macaques
  • 01/01/2020 - The RepID-CRL4 ubiquitin ligase complex regulates metaphase to anaphase transition via BUB3 degradation
  • 12/01/2019 - Radiation drives the evolution of orthotopic xenografts initiated from glioblastoma stem-like cells
  • 12/01/2019 - Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans
  • 11/01/2019 - CRISPR/Cas9-mediated knockout and in situ inversion of the ORF57 gene from all copies of the Kaposi's Sarcoma-Associated Herpesvirus genome in BCBL-1 cells
  • 08/01/2019 - Genomic profiling of primary histiocytic sarcoma reveals two molecular subgroups
  • 05/01/2019 - Relationship between human leukocyte antigen alleles and risk of Kaposi's sarcoma in Cameroon
  • 01/01/2019 - Lysyl Oxidase Is a Key Player in BRAF/MAPK Pathway-Driven Thyroid Cancer Aggressiveness
  • 01/01/2019 - Distinct genome-wide methylation patterns in sporadic and hereditary nonfunctioning pancreatic neuroendocrine tumors
  • 12/01/2018 - Baseline Intrahepatic and Peripheral Innate Immunity are Associated with Hepatitis C Virus Clearance During Direct-Acting Antiviral Therapy
  • 11/01/2018 - Murine pre-B-cell ALL induces T-cell dysfunction not fully reversed by introduction of a chimeric antigen receptor
  • 11/01/2018 - NPHS2 V260E is a frequent cause of steroid-resistant nephrotic syndrome in Black South African children
  • 10/01/2018 - Metastatic adrenocortical carcinoma displays higher mutation rate and tumor heterogeneity than primary tumors
  • 09/01/2018 - Fetal-not maternal APOL1 genotype associated with risk for preeclampsia in those with African ancestry

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