Transcriptomics Explorer

Topic	Replies	Views	Activity
Extracting data from whole cortex+hippocampus transcrip.tome data set anatomy , celltype , analysis , how-to	1	985	November 19, 2019
Metadata of mouse whole cortex and hippocampus 10x data set	6	815	September 8, 2021
What brain regions are denoted as M1ul/M1lm and S1ul/S1lm? atlas-cell-types , anatomy , analysis	1	1157	April 27, 2020
Getting Started: Gene Expression Heatmap	0	1322	August 12, 2020
List of Cell-Type and/or Cluster Markers transcriptomics , celltype , analysis , how-to	4	942	August 9, 2022
Getting Started with the Transcriptomics Explorer Overview The Transcriptomics Explorer is a browser-based tool for researchers to visualize and analyze scRNA sequencing data and related cell types for both mouse and human. A previous version of this tool - called the …	3	1838	March 21, 2023
How do I find genes that differentiate Cell Types? (differential search) transcriptomics_explorer	0	652	September 17, 2019
Citation for Allen scRNAseq Mouse and Human datasets transcriptomics , rna-seq , publication	4	1570	March 30, 2020
How to set median data in transcriptomics explorer in human datasets? atlas-human-brain-adult , transcriptomics , how-to , human	8	1017	November 3, 2020
Getting Started: Dataset Sampling Strategy	0	481	August 12, 2020
CPM normalization of 10X mouse single-cell RNA-seq	2	1371	August 25, 2021
From electrophysiology to t-types celltype , analysis	2	686	August 7, 2020
How to set median data in transcriptomics explorer in mouse datasets? atlas-mouse-brain-adult , transcriptomics , how-to	4	671	July 12, 2020
Is the previous version of the site still available somewhere? analysis , how-to	2	837	January 7, 2020
Non-anonymized BAM files transcriptomics , analysis , how-to , rna-seq , human , alzheimers	1	901	March 26, 2020
How to convert scRNA gene names to common gene IDs? analysis	2	733	October 8, 2020
PKM Splice Variants transcriptomics , rna-seq	1	850	November 26, 2020
Human dopaminergic neurons atlas-cell-types , atlas-human-brain-adult , transcriptomics , celltype , analysis	2	645	November 12, 2020
Transcriptomic explorere missing information? atlas-cell-types , transcriptomics , analysis , how-to	1	776	October 21, 2020
Can we download a Heat Map or t-SNE visualisation? atlas-cell-types , analysis , how-to , software	1	749	May 8, 2020
Reconstructing the dendrogram shown in the transcriptomics explorer with R based on the .json file transcriptomics , analysis , how-to , software	1	741	October 27, 2020
Comparing expression of a subset of genes in a subset or areas across cell types how-to	5	230	September 9, 2024
Getting Started: Scatterplot (tSNE or UMAP)	0	992	August 12, 2020
Is there a way to associate median-cluster cell type aliases with their structure ids? atlas-cell-types , anatomy , how-to	2	544	May 4, 2021
Subsetting Mouse Whole Cortex and Hippocampus 10x data by brain region? atlas-mouse-brain-adult	1	546	July 7, 2023
How do I find marker genes for a Cell Type or Cell Set? transcriptomics_explorer	0	725	September 17, 2019
Is there a way to subset ORB from PL;ILA;ORB?	1	498	August 11, 2022
Does Allen brain provide user open source to build transcriptomics explorer?	1	476	July 24, 2020
Can I map my own data to these data sets? transcriptomics_explorer	0	631	September 17, 2019
What datasets are available in the Transcriptomics Viewer?	0	541	September 3, 2019
New Genome Browser views for single cell/nucleus transcriptomics! celltype , rna-seq	0	540	January 13, 2021
Supported browsers	0	517	February 7, 2020
Human Forebrain Genome Data	1	299	March 14, 2023
Known protein not detected by RNA explorer rna-seq	1	167	February 29, 2024
Cell Types Database: RNA-Seq Data	1	104	March 14, 2025
RNA expression values on heat map Developmental Transcriptome do not match database atlas-human-brain-developing	3	62	October 31, 2025
Ensembl ID and gene name not matching transcriptomics , rna-seq	1	81	September 26, 2025
Connectivity.brain-map.org still down / blank page as of November 2025	2	50	November 15, 2025
Deconvolution of mice bulk hippocampal transcriptomics	1	27	January 12, 2026
Seeking Single-Cell Expression Data in Intergenic Regions	1	26	January 17, 2025
Gene Thresholds	1	23	March 27, 2026

Extracting data from whole cortex+hippocampus transcrip.tome data set

1

985

November 19, 2019

Metadata of mouse whole cortex and hippocampus 10x data set

6

815

September 8, 2021

What brain regions are denoted as M1ul/M1lm and S1ul/S1lm?

atlas-cell-types , anatomy , analysis

1

1157

April 27, 2020

Getting Started: Gene Expression Heatmap

0

1322

August 12, 2020

List of Cell-Type and/or Cluster Markers

transcriptomics , celltype , analysis , how-to

4

942

August 9, 2022

Getting Started with the Transcriptomics Explorer

Overview The Transcriptomics Explorer is a browser-based tool for researchers to visualize and analyze scRNA sequencing data and related cell types for both mouse and human. A previous version of this tool - called the …