velodyn | Dynamical systems methods for RNA velocity analysis | Genomics library

 by   calico Python Version: 0.1.0 License: Apache-2.0

kandi X-RAY | velodyn Summary

kandi X-RAY | velodyn Summary

velodyn is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. velodyn has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install velodyn' or download it from GitHub, PyPI.

RNA velocity infers a rate of change for each transcript in an RNA-sequencing experiment based on the ratio of intronic to exonic reads. This inferred velocity vectors serves as a prediction for the future transcriptional state of a cell, while the current read counts serve as a measurement of the instantaneous state. Qualitative analysis of RNA velocity has been used to establish the order of gene expression states in a sequence, but quantitative analysis has generally been lacking. velodyn adopts formalisms from dynamical systems to provide a quantitative framework for RNA velocity analysis. The tools provided by velodyn along with their associated usage are described below. All velodyn tools are designed to integrate with the scanpy ecosystem and anndata structures. We have released velodyn in association with a recent paper. Please cite our paper if you find velodyn useful for your work. Differentiation reveals latent features of aging and an energy barrier in murine myogenesis Jacob C Kimmel, Nelda Yi, Margaret Roy, David G Hendrickson, David R Kelley Cell Reports 2021, 35 (4); doi: If you have any questions or comments, please feel free to email me. Jacob C. Kimmel, PhD jacobkimmel+velodyn@gmail.com Calico Life Sciences, LLC.
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            kandi-support Support

              velodyn has a low active ecosystem.
              It has 15 star(s) with 1 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              velodyn has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of velodyn is 0.1.0

            kandi-Quality Quality

              velodyn has no bugs reported.

            kandi-Security Security

              velodyn has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              velodyn is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              velodyn releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed velodyn and discovered the below as its top functions. This is intended to give you an instant insight into velodyn implemented functionality, and help decide if they suit your requirements.
            • Sample velocity estimates for each gene
            • Sample the matrix
            • Fit the velocity matrix to a set of counts
            • Sample a single cell
            • Samples the counts from spliced reads
            • Sample the abundance profile
            • Compute the divergence of an embedding matrix
            • Compute the velocity of a grid on a grid
            • Compute the divergence of a vector field
            • Simulate phase points
            • Evaluate the phase at x0
            • Predict the derivative of the model
            • Fit the model using KNeighborsRegressor
            • Make argument parser
            • Add argument specific to the parser
            Get all kandi verified functions for this library.

            velodyn Key Features

            No Key Features are available at this moment for velodyn.

            velodyn Examples and Code Snippets

            Tutorial,State transition rate comparisons with phase simulations,Usage
            Pythondot img1Lines of Code : 31dot img1License : Permissive (Apache-2.0)
            copy iconCopy
            from velodyn.velocity_dynsys import PhaseSimulation
            
            simulator = PhaseSimulation(
                adata=adata,
            )
            # set the velocity basis to use
            simulator.set_velocity_field(basis='pca')
            # set starting locations for phase points
            # using a categorical variable in  
            VeloDyn -- Quantitative analysis of RNA velocity
            Pythondot img2Lines of Code : 17dot img2License : Permissive (Apache-2.0)
            copy iconCopy
            @article{kimmel_latent_2021,
            	title = {Differentiation reveals latent features of aging and an energy barrier in murine myogenesis},
            	volume = {35},
            	issn = {2211-1247},
            	url = {https://www.cell.com/cell-reports/abstract/S2211-1247(21)00362-4},
            	doi   
            Tutorial,Velocity confidence intervals,Usage
            Pythondot img3Lines of Code : 13dot img3License : Permissive (Apache-2.0)
            copy iconCopy
            from velodyn.velocity_ci import VelocityCI
            
            # initialize velocity CI
            vci = VelocityCI(
                adata=adata,
            )
            # sample velocity vectors
            # returns [n_iter, Cells, Genes]
            velocity_bootstraps = vci.bootstrap_velocity(
                n_iter=n_iter,
                save_counts=out_  

            Community Discussions

            QUESTION

            Why is RVIZ telling me that there is "No transfrom from [velodyne] to [base_link]" even though I have such a joint defined in my URDF?
            Asked 2021-Jun-02 at 21:09

            RVIZ is telling me that there is "No transfrom from [velodyne] to [base_link]". I have a joint between these two objects defined in my URDF file:

            ...

            ANSWER

            Answered 2021-Jun-02 at 21:09

            You will need to launch a robot_state_publisher node that publishes the tf transforms between your different links in any case - even if your links are connected with fixed joints only. Therefore either add

            Source https://stackoverflow.com/questions/67756243

            QUESTION

            How do I get the orientation from a open3d.geometry.OrientedBoundingBox?
            Asked 2021-Mar-21 at 20:50

            I've created a Oriented Bounding Box from a clustered sub point cloud of a Velodyne Lidar (rotating laser sensor). I want to get the orientation of the Bounding Box (preferable as a quaternion).

            ...

            ANSWER

            Answered 2021-Mar-21 at 20:50

            Looking at the link you shared, I see the OBB object has the following properties: center, extent and R. If you can access them then you can get position and orientation. Center is a point (x,y,z), extent are three lengths in x, y and z direction and R is a rotation matrix. Columns of R are three orthogonal unit-vectors pointing on rotated x, y and z directions.

            I think you are interested in orientation, so R is the orientation matrix. You can convert it to quaternion using the matrix-to-quaternion method on this page: https://www.euclideanspace.com/maths/geometry/rotations/conversions/matrixToQuaternion/

            Source https://stackoverflow.com/questions/66712854

            QUESTION

            Reading Point Cloud .bin file using C++
            Asked 2021-Jan-05 at 00:13

            I'm trying to read .bin point cloud files. I found this link suggesting a python code that I can convert to C++. I came up with the following code, but the precision of the floating point numbers are different compared to the results that I got from running the python code in the above link. I noticed that some coordinate values in the middle are totally missing, or in other words, the count of the floating point values that resulted from python is more than that of the C++ code:

            ...

            ANSWER

            Answered 2021-Jan-05 at 00:13

            Here's a code that produces exactly the same output as the Python version:

            Source https://stackoverflow.com/questions/65570879

            QUESTION

            how to display velodyne points on ROS installed on "Ubuntu on Mac" via Parallels Desktop on macOS?
            Asked 2020-Jun-23 at 20:51

            This is probably easy but I am a noob in networks so please help! Basically I am trying to display lidar points from my Velodyne VLP-16 on ROS installed on Ubuntu 18.04 which is in turn installed via Parallels Desktop on my macOS.

            So I plugged the velodyne's ethernet cable to my MacBook via a usb-C-to-ethernet adapter and set this on my mac:

            I can type in my browser this address 192.168.1.201 and I can see the velodyne interface. So it works.

            When I now go to "Ubuntu on Mac" via Parallels Desktop and do not change anything in Network->Settings->Wired->Connected so I can see these settings:

            ... I can still see the velodyne interface via a browser on Ubuntu by typing the 192.168.1.201 address as I can on macOS. The only problem is that when I wanna run

            ...

            ANSWER

            Answered 2020-Jun-23 at 20:51

            After a thorough examination of the network traffic both on macOS and on the emulated Ubuntu using Wireshark on both ends, I realised that there is no Network adapter present in the virtual machine configuration.

            Following the answer from Desktop Parallel support, I did: Ubuntu on Mac -> configure -> hardware -> add device -> network 2 -> source: USB...

            and when you check now in Wireshark, you will see the traffic coming from the USB adapter and the ROS driver, via an adequate port, will capture the packets.

            Source https://stackoverflow.com/questions/62525243

            QUESTION

            How to keep NVCC from generating compatibility for other 11 SM architectures?
            Asked 2020-Feb-03 at 06:11

            When I build PCL library on Jetson TX2 from source via CMAKE, I get the following debug logs among other msgs:

            ...

            ANSWER

            Answered 2020-Feb-03 at 06:11

            I found a file which was causing the CMAKE to include 10 sm_arch in compatibility list. Here's the link. I will re-compile after editing the file for just 1 sm_arch and compare the size of binaries generated. – Anuj Patil Jan 22 at 18:10

            So findCUDA was the culprit here. Editing the files to required sm_arch does the trick!

            Source https://stackoverflow.com/questions/59863431

            QUESTION

            Bash-Ubuntu 18.04-ROS-Melodic: Ping to IP address does not return anything
            Asked 2019-Dec-31 at 08:35

            I have a Velodyne Puck 16 sensor that I have been trying to connect to ROS Melodic for the past few days. My OS is Ubuntu 18.04. I was able to find out the address of the lidar using WireShark, as it is possible to see below:

            So the IP is: 10.0.1.201

            After very very carefully following the installation procedure in the official documentation everything I was trying was unsuccessful.

            So I decided to apply a simple ping procedure to the address of the lidar:

            ping 10.0.1.201 it does not return any package of information despite it seems connected.

            The problem I have is that, despite I know the IP address of my Velodyne 16 using Wireshark, the lidar does not answer to a simple test as the ping of the id.

            Steps I followed: 1 Configure your computer’s IP

            Below the connection procedure: I created a velodyne_interface connection, see below:

            Existing Connection

            velodyne_interface

            2 Connecting your computer to LIDAR through terminal ...

            ANSWER

            Answered 2019-Dec-31 at 08:35

            There is probably some problems with the routing. You can try debugging the routing issues, some googling will probably help there. Some commands which might help pinpoint the problem tracepath -n 10.0.1.201 and ip route list.

            The easiest solution to your problem would be to just configure the "velodyne_interface" you created to the same subnet as your velodyne lidar. So in the "velodyne_interface" set your ip to 10.0.1.20 for example. Connect to the "velodyne_interface" connection, verify that you have the ip you set by typing ip a or ifconfig in some terminal and you should be able to access the Velodyne web interface from 10.0.1.201. From there you can configure the velodyne sensor networking to the settings you like.

            Source https://stackoverflow.com/questions/59471188

            QUESTION

            How to playback Lidar pointcloud from bag file in ros, rviz?
            Asked 2019-Oct-14 at 06:57

            I got a bag dataset and want to play the message containing velodyne VLP-16 points back. But got uncomplete result.

            I've tried: - increasing fps in rviz - using timestamp from other simulation

            I expect to got uncut result / a ring of lidar radius beam.

            This is the result I got in rviz result

            ...

            ANSWER

            Answered 2019-Oct-14 at 06:57

            As you can see, the points are available but they are not visible long enought because points are not showed simultaneously. The reason is that a single message does not contain all points of a complete (360°) beam. A beam gets splittet to several messages typically, of which only the latest gets shown by default. Checking the rviz point cloud documentation you will find a parameter called decay time:

            The amount of time to keep a cloud/scan around before removing it. A value of 0 means to only display the most recent data.

            Try increasing the value of this parameter in rviz, then you should be able to see more points simultaneously.

            Source https://stackoverflow.com/questions/58362870

            QUESTION

            What are the contents of PointCloud2?
            Asked 2019-Sep-12 at 11:08

            What does the contents of PointCloud2 means in ROS?

            1. fields.offset?
            2. fields.datatype?
            3. fields.count?
            4. point_step?
            5. row_step?

            Its documentation is poor

            Here is a published PointCloud2 message by Velodyne LiDAR:

            ...

            ANSWER

            Answered 2019-Sep-12 at 11:08

            Maybe I'm a bit late, but for anybody having the same Problem:

            For question 1.-3. see this. Also what you need to have in mind, is that the data is stored as uint8, but your points should be in float32, if I see it correctly. Therefore each value (x,y,z,intensity, etc.) or "field" is stored as multiple uint8 bytes. So you need 4 data entries to represent the x value of one point. The total length of one point in bytes is stored as "point_step", answering your fourth question.

            1. The Field Offset is the number of bytes from the start of the point to the byte, in which this field begins to be stored. So every point has the first 4 bytes for x, then with an offset of 4 start the bytes for y etc.

            2. and 3.: fields.datatype and fields.count: See this

            3. point.step is number of bytes or data entries for one point

            4. row_step: See your own link, so it is "number of points per row * point_step"

            5. Probably your scanner publishes line after line? I'm actually not sure of this one.

            6. No, the first 4 entries represent the x value, so 235, 171, 190, 53 equals: 11101011 10101011 10111110 00110101 and this represents a float32 value. The 171 has no direct information about the x, y or z value of the point.

            Source https://stackoverflow.com/questions/57507876

            QUESTION

            Projection of 3D Lidar point in the i-th camera image (KITTI Dataset)
            Asked 2019-May-29 at 15:55

            I am working on a object classification problem and I am using Lidar and camera data from the Kitti Dataset., In this article : http://ww.cvlibs.net/publications/Geiger2013IJRR.pdf , they provide the formulas for projecting the 3d PointCloud into the i-th camera image plane, but I don't understand some things :

            Following equation((3) :

            If the 3D point X is in velodyne camera image and Y in the i'th camera image, why X has four coordinates and Y three? It should have been 3 and 2, no?

            I need to project the 3D point Cloud into the camera image plane for then creating lidar images to use them as a channel for the CNN. Anyone who has ideas for it ?

            Thanks you in advance

            ...

            ANSWER

            Answered 2019-May-29 at 15:55

            For your first query regarding x and y dimension there are two explanation.

            Reason 1.

            • For image re-projection pin hole camera model is used which is in perspective coordinate or homogenous coordinate. Perspective projection uses the image origin as centre of projection and points are mapped to the plane z=1. A 3D point [x y z] is represented by [xw yw zw w] and the point it maps on the plane is represented by [xw yw zw]. Normalising with w gives.

              So (x,y) -> [x y 1]T : Homogeneous Image Coordinates

              and (x,y,z) - > [x y z 1] T : Homogeneous Scene Coordinates

            Reason 2.

            • With respect to the paper you have attached, considering equation (4) and (5)

              It is clear that P is of dimension 3X4 and R is expanded to 4x4 dimension.Also x is of dimension 1x4. So as per matrix multiplication rule number of columns of first matrix must equal to the number of rows of second matrix. So for given P of 3x4 and R of 4x4, x has to be 1x4.

            Now coming to your second question of LiDAR image fusion, It requires intrinsic and extrinsic parameters (relative rotation and translation) and camera matrix. This rotation and translation forms a 3x4 matrix called as transformation matrix. So the point fusion equations becomes

            Source https://stackoverflow.com/questions/56355893

            QUESTION

            Filling MRPT velodyne scan observation
            Asked 2018-Nov-25 at 04:22

            I'm new to MRPT and I would like to use it for building an occupancy grid map using velodyne point clouds.

            The KITTI dataset provide velodyne point clouds in (x,y,z,r) format, where r is the reflectance. I'm trying to fill a mrpt::obs::CObservationVelodyneScan with such data, but using insertObservation method seems to do just nothing. Can you point me in the right direction for using this observation type?

            My code basically looks like this:

            ...

            ANSWER

            Answered 2018-Nov-25 at 04:22

            I was these days also working on the Kitti dataset, so I just added a new function to load a kiti velodyne data file directly into MRPT (see this PR).

            However, after some thinking, I noticed that Kitti raw data does not match exactly with CObservationVelodyneScan, which is aimed at storing the raw ranges for each LiDAR beam, and only optionally, a pointcloud. The Kitti velodyne data are pointclouds, actually, hence I added a new PointCloud type with XYZ+Intensity mrpt::maps::CPointsMapXYZI and added a method loadFromKittiVelodyneFile() to it. Notice this is for the mrpt master git branch, "version 1.9.9".

            Now, how to insert that into a gridmap? Your idea of using a velodyne CObservation to insert it into a gridmap is one of the pending issues on our queue but, anyway, as said above, the Kitti datasets are better loaded as pointclouds.

            I would recommend you converting the pointcloud into a CObservation2DRangeScan, then inserting it into the grid. That would allow you to control what part of the 3D data you really want to be reflected in the grid (i.e. what heights, etc.)

            Hope it helped!

            Source https://stackoverflow.com/questions/53444024

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install velodyn

            You can install using 'pip install velodyn' or download it from GitHub, PyPI.
            You can use velodyn like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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