Contributors:Filipe, Martin Journois, Frank, Rob Story, James Gardiner, Halfdan Rump, Andrew Bird, Antonio Lima, Joshua Cano, dbf, Juliana Leonel, Tim Sampson, Jason Baker, Ben Welsh, Jon Reades, Oleg Komarov, Qingkai Kong, odovad, Raphael Dumas, George Harris, Alex Crosby, Leonardo Furtado, kenmatsu4, Tales Paiva Nogueira, Nat Wilson, penguindustin, Daisuke Kato, Rich Signell, Justin Duke, Anand Patil
Upgrade Leaflet 1.5.1 -> 1.6.0 (@conengmo #1241)
Add auto_start parameter to locate control plugin (@fullonic #1220)
New feature: GeoJsonPopup (@jtbaker #1023)
Choropleth: default color for with and without data (@conengmo #1288)
Update WMS data url in WmsTimeDimension example notebook (@sknzl #1259)
Search plugin: fix position argument (@jjbenes #1304)
Fix GeoJsonPopupAndTooltip example notebook (@conengmo #1298)
Change geopandas dataframe to_crs() usage syntax (@artnikitin #1251)
GeoJson: fix show parameter when embedding data (@conengmo #1289)
Use https CDN for leaflet.timedimension.control.min.css (@sknzl #1256)
Host leaflet-heatmap.js under different name to avoid adblockers (@conengmo #1240)
Removed unused folium.utilities.iter_points function, use instead iter_coords (@conengmo #1294)
Contributors:Bull, Daniel, Smethurst, Joel A, Sinclair, Ian, Pierron, Fabrice, Roose, Tiina, Powrie, William, Bengough, Glyn
Collection of data files used in the paper titled: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation.
Additional dataset which covers the noise study CT scans and digital volume correlation noise studies can be found in DOI: 10.5281/zenodo.3361832
Data contains the following:
X-ray CT data for the interrupted direct shear tests of a soil sample containing a Willow plant. The first file is the specimen scanned unloaded, followed by seven incremental shear load steps to 20 mm shear displacement. Files are 8-bit unsigned and 1800x1800x1600px. Voxel resolution is 0.04642 mm.
Direct shear vs. displacement data is presented in an Excel spreadsheet:
Normal and shear strain DVC data which has been averaged and plotted against specimen depth is presented in an Excel spreadsheet:
CT scan metadata giving information to the scan settings, voxel resolution, etc. is contained in a .zip file which consists of .xtekct and .XML files generated from the Nikon CT scanner.
Drawings and Solidworks CAD files of the direct shear test rig are contained within the .zip file. There are a number of parts to the assembly. The file SSSB1003-5.SLDASM contains the complete assembly of the direct shear rig and will help identify the part names. The folder CAD_Drawings contains pdf documents of the part drawings.
Tabulated DVC data taken at 32x32x32px subset size is contained inside a .zip file. These consist of tab separated .dat files from unloaded (data_1.dat) through incremental load steps Load A, Load B... Load G, (data_2.dat, data_3.dat... data_8.dat). The structure of the .dat file contains columns of data with each column number corresponding to the following: (1) x, (2) y (3) z, (4) vx, (5) vy, (6) vz, (7) exx, (8) eyy, (9) ezz, (10) exy, (11) exz, (12) eyz, (13) volumetric strain, (14) is valid. Columns 1-3 are subset positions in mm, 4-6 are displacements in mm, 7-9 are normal strains, 10-12 are shear strains, 13 is volumetric strain and 14 is a binary value indicating if the subset is valid.
Tabulated DVC data applied to the load step CT data at 32, 48, 64, 96, 128 pixels is presented in the .zip files containing .dat tab separated files. The structure of the .dat files is described in the previous bullet point. These files were used to construct the noise study applied to incrementally loaded CT data by sampling regions away from the shear zone where the strain signals are close to zero.
Processed noise study data which compares the effects of DVC subset size is presented in the .xlsx file. This file contains both the controlled noise experiment data (stationary, magnification and rigid body motion) and noise study data applied to incrementally loaded data using sampled regions away from the shear zone where the strain signals are close to zero.
Tabulated data which compares the local x displacement vs depth profile from DVC and direct measurement of root position is contained in the following Excel spreadsheet file:
Compressed fastqs for raw sequences of clinical isolates of Escherichia coli infection from Toronto, Canada in 2018 (Dataset 2). Sequencing details outlined in associated publication. Performed using Illumina NextSeq platform.
This repository makes available the processed data and the results of our SURF paper.
The paper presents the Statistical Utility for RBP Functions (SURF) for integrative analysis of RNA-seq and CLIP-seq data. The goal of SURF is to identify alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs and elucidate protein-RNA interactions governing these events. We applied the SURF pipeline to analyze 104 RBP data sets (from ENCODE) and performed downstream analysis. Check out the browsable results from this shiny app!
The current repository includes:
meme.326.input.zip -- input of 326 MEME runs on SURF-inferred location features
meme.326.output.zip -- output of 326 MEME runs on SURF-inferred location features
surf_inferred_feature.gtf -- SURF-inferred location features for 52 RBPs
gencode.v24.annotation.filtered.gtf -- filtered genome annotation used for ENCODE data analysis
Homo_sapiens.GRCh37.71.primary_assembly.protein_coding.gtf -- genome annotation used for simulation study
simulation_truth.txt -- truth parameters used for RNA-seq simulation
[RBP].results.rds -- SURF output (each an R object) for 104 RNA-binding proteins ([RBP] the protein name).
For reproducing the results, the source code is available at DOI: 10.5281/zenodo.3779853.