Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Summer 6, Summer 7
Description
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site.
Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments.
Then, make it possible for other people to also open the file and view the contents in IGB.
Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3765 [ 22984 ] |
| Summary | Obtain a file containing sequence read alignments for Suerat vignette | Obtain and view sequence read alignments for PMBC dataset from Seurat vignette |
| Assignee | Ann Loraine [ aloraine ] |
| Description |
For this task, locate a BAM or FASTQ format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Suerat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use R to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use R to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. |
| Description |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use R to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. |
| Description |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Description |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Then, make it possible for other people to also open the file and view the contents in IGB. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. |
| Attachment | quickload.zip [ 18464 ] |
| Summary | Obtain and view sequence read alignments for PMBC dataset from Seurat vignette | Obtain and view sequence read alignments for PBMC dataset from Seurat vignette |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Sprint | Summer 6 [ 200 ] | Summer 6, Summer 7 [ 200, 201 ] |
| Rank | Ranked higher |
| Attachment | 2024-08-12-IQSEC1-PBMC-scRNA-Seq.png [ 18465 ] |
| Attachment | 2024-08-12-IQSEC1-PBMC-scRNA-Seq.png [ 18465 ] |
| Attachment | 2024-08-12-IQSEC1-PBMC-scRNA-Seq.png [ 18466 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Description |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Then, make it possible for other people to also open the file and view the contents in IGB. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Then, make it possible for other people to also open the file and view the contents in IGB. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. 10X data: https://www.10xgenomics.com/datasets/3-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0 |
| Attachment | quickload.zip [ 18464 ] |
| Attachment | quickload.zip [ 18467 ] |
| Description |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Then, make it possible for other people to also open the file and view the contents in IGB. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. 10X data: https://www.10xgenomics.com/datasets/3-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0 |
For this task, locate a BAM format data files for the RNA-Seq data set described in this Seurat tutorial:
* https://satijalab.org/seurat/articles/pbmc3k_tutorial The above tutorial demonstrates features of the Seurat single-cell RNA-Seq data analysis library using data from peripheral blood mononuclear Cells (PBMC) originally from the 10X Genomics Web site. Open the data file in IGB. Use the Seurat library (in R) to locate some genes with high counts and then check that IGB shows the same or similar numbers of read alignments. Then, make it possible for other people to also open the file and view the contents in IGB. Note: If you get stuck on figuring out how to use Seurat for this, ask for help from one of our many local R experts. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Karthik Raveendran [ karthik ] |