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Publication Year: 2021

151 to 160 of 286 Results

PHIM_xisRNA_MS_dataverse_code.Rmd Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection" R Markdown Text - 324.6 KB - MD5: ede28f634dc2712e930c4d8c3783e472 CodeDocumentation This R Markdown file records the code of most secondary analysis computing tasks performed to generate the material that is relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. The accompanying html file was generated using this rmd file.
PHIM_ xisRNA_session.RData Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection" R Data - 849.4 MB - MD5: d52bc72c86361b747f98eb875e13a00d Data R statistical programming language RData file storing the objects created for the production of the "PHIM_ xisRNA_MS_dataverse_code.html" file using the R code found in the html file itself as well as in the "PHIM_ xisRNA_MS_dataverse_code.Rmd" R Markdown file.
Anthropogenic_fibers_in_clams_ number_size_colour.tab Sep 10, 2021 - Anthropogenic fibers (quantity, size, colour) observed in whole body, gills, digestive glands and remaining tissues of Asiatic Clam (Meretrix Lyrata) sampled in Can Gio mangrove, Ho Chi Minh City, Viet Nam in 2016 Tabular Data - 42.3 KB - 29 Variables, 434 Observations - UNF:6:RrihjsHtZvPcS5vxn5fRgQ== Data Size and colour of anthropogenic fibers observed in each pooled clam and in specific dissected part of the clam are given.
Clam_dissection_data_dictionary.txt Sep 10, 2021 - Anthropogenic fibers (quantity, size, colour) observed in whole body, gills, digestive glands and remaining tissues of Asiatic Clam (Meretrix Lyrata) sampled in Can Gio mangrove, Ho Chi Minh City, Viet Nam in 2016 Plain Text - 772 B - MD5: 0afa383dc59a4e9fb6059fbba9b8a285 Documentation Data dictionary
Clams_information_data_dictionary.txt Sep 10, 2021 - Anthropogenic fibers (quantity, size, colour) observed in whole body, gills, digestive glands and remaining tissues of Asiatic Clam (Meretrix Lyrata) sampled in Can Gio mangrove, Ho Chi Minh City, Viet Nam in 2016 Plain Text - 781 B - MD5: 9292e760b3c670a045a8f52676a1aefc Documentation Data dictionary
Clams_information.tab Sep 10, 2021 - Anthropogenic fibers (quantity, size, colour) observed in whole body, gills, digestive glands and remaining tissues of Asiatic Clam (Meretrix Lyrata) sampled in Can Gio mangrove, Ho Chi Minh City, Viet Nam in 2016 Tabular Data - 11.7 KB - 8 Variables, 112 Observations - UNF:6:yAB4vK7/mYnTjBHF3l0IOQ== Data Sampled clams details (length, mass)
1_TtmappednewTtvar_biallelic.vcf.gz Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins Gzip Archive - 704.4 MB - MD5: 4461877afe51bc505f570808593aa7c0 Data Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation.
2_Tursiops_unlinkedSNPs.beagle.gz Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins Gzip Archive - 85.1 MB - MD5: 8fe3f103955bdd7dd145c316dc008fe6 Data Genotype likelihood LD pruned input file in Beagle format. Note that Sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and...
3_Tursiops_ALL.haplo.gz Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins Gzip Archive - 108.0 MB - MD5: e7909efb3649e2ac35f3cb17268be917 Data haplo file (pseudo-haploid random call): samples order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included, but was not included in the analyses, which are based on subset of individuals (one coastal individual and all allopatric pelagic individuals except from...
4_GhostAncestry-master.tar.gz Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins Gzip Archive - 8.8 KB - MD5: d5234dbb967ad08679ed0eb346e3308e Code GhostAncestry-master contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only #...

PHIM_xisRNA_MS_dataverse_code.Rmd

Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

R Markdown Text - 324.6 KB -

CodeDocumentation

This R Markdown file records the code of most secondary analysis computing tasks performed to generate the material that is relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. The accompanying html file was generated using this rmd file.

PHIM_ xisRNA_session.RData

Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

R Data - 849.4 MB -

Data

R statistical programming language RData file storing the objects created for the production of the "PHIM_ xisRNA_MS_dataverse_code.html" file using the R code found in the html file itself as well as in the "PHIM_ xisRNA_MS_dataverse_code.Rmd" R Markdown file.

Anthropogenic_fibers_in_clams_ number_size_colour.tab

Sep 10, 2021 - Anthropogenic fibers (quantity, size, colour) observed in whole body, gills, digestive glands and remaining tissues of Asiatic Clam (Meretrix Lyrata) sampled in Can Gio mangrove, Ho Chi Minh City, Viet Nam in 2016

Tabular Data - 42.3 KB - 29 Variables, 434 Observations -

Data

Size and colour of anthropogenic fibers observed in each pooled clam and in specific dissected part of the clam are given.

Clam_dissection_data_dictionary.txt

Plain Text - 772 B -

Documentation

Data dictionary

Clams_information_data_dictionary.txt

Plain Text - 781 B -

Documentation

Data dictionary

Clams_information.tab

Tabular Data - 11.7 KB - 8 Variables, 112 Observations -

Data

Sampled clams details (length, mass)

1_TtmappednewTtvar_biallelic.vcf.gz

Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Gzip Archive - 704.4 MB -

Data

Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation.

2_Tursiops_unlinkedSNPs.beagle.gz

Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Gzip Archive - 85.1 MB -

Data

Genotype likelihood LD pruned input file in Beagle format. Note that Sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and...

3_Tursiops_ALL.haplo.gz

Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Gzip Archive - 108.0 MB -

Data

haplo file (pseudo-haploid random call): samples order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included, but was not included in the analyses, which are based on subset of individuals (one coastal individual and all allopatric pelagic individuals except from...

4_GhostAncestry-master.tar.gz

Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Gzip Archive - 8.8 KB -

Code

GhostAncestry-master contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only #...

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