v1.7.1

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

v0.99.15

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

v0.99.13

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

v.0.99.12

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o Seven new loadable objects are available in the package.
o The new readSNVVCF() function enable the use of VCF SNP files as input for the runExomeAncestry() and runRNAAncestry() functions.

v0.99.11

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o The main vignette has been updated.

v0.99.10

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o The main vignette has been updated.

v0.99.8

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o The new runRNAAncestry() function executes most steps leading to the ancestry inference call on a specific RNA profile.
o A vignette describing the Reference GDS files has been created.

v0.99.5

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o The function documentation has been improved.
o New vignette has been created. The vignette covers the steps done by the runExomeAncestry() function.

v0.99.4

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o The number of visible functions has been limited to simplify usage.
o The function documentation has been improved.
o A wrapper function is now available.

v0.99.0

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

SIGNIFICANT USER-VISIBLE CHANGES

o The number of visible functions has been limited to simplify usage.