The public repository for collecting Enrichr-related issues, questions and suggestions.
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Explain how the statistics are done
Thanks so much for producing Enrichr. It's an amazing tool.
Every tab provides an odds ratio and a p-value. It would be good in the FAQ to explain what type of statistics go into those calculations. It would make Enrichr less of a black box.
Thanks again!
gene names in gwas catalog 2019
Describe the bug
Possible Excel conversion in gene names in gwas catalog library
To Reproduce
Steps to reproduce the behavior:
- Go to https://maayanlab.cloud/Enrichr/#stats
- Click on GWAS catalog 2019
- search for 1-MAR, 1-DEC
Expected behavior
I think these names got converted by Excel, probably only in this file and not in the application. The correct gene name should be MARCH1
[BUG]
Describe the bug
The EnrichR webpage used to have a place to upload the genes as a file and now it has disappeared (for some time now).
To Reproduce
Go to EnrichR webpage and try to input the genes as a file.
Expected behavior
To have Choose File button that used to be there and it isn't anymore.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
Gene search for GTEx aging genes does not work properly
To Reproduce
Steps to reproduce the behavior:
- Go to Gene Search
- Type LGI3
- Scroll down to 'GTEx aging libraries'
- See error
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
[BUG]It would be good to accept all common types of IDs
Describe the bug
A clear and concise description of what the bug is.
This is not a bug. But I think for biologists, who are not familiar with bioinformatics, it would be a perfect enrichment tool if it can accept kinds of IDs from various databases, such as ensemble gene ids, ncbi entrez gene accession, Affymetrix probes, etc. What the database maintainers need to do is to add a step to transform the submitted ids into the database recognizing ids, i.e. gene symbols, before the enrichment analysis.
To Reproduce
Steps to reproduce the behavior:
- Go to '...'
- Click on '....'
- Scroll down to '....'
- See error
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
[BUG] Incorrect CORS header setting (or policy change?)
Describe the bug
Before the migration to the new domain (http://maayanlab.cloud), our web application works perfectly when it calls Enrichr API for enrichment analysis on-the-fly. However, this week, we noticed the old API no longer works. We updated the URLs to the new ones in our application and "sometimes" it worked, but now it cannot access it anymore due to the following issue:
Access to fetch at 'http://maayanlab.cloud/Enrichr/addList' from origin 'http://hiview.ucsd.edu' has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource. If an opaque response serves your needs, set the request's mode to 'no-cors' to fetch the resource with CORS disabled.
Is this a policy change to block some of the 3rd party web applications or CORS setting has been misconfigured during the migration to new domain?
To Reproduce
Steps to reproduce the behavior:
Just call any API from JS code deployed as a part of web application. All of them fails with the CORS header problem.
Expected behavior
Allow web application to access API without CORS error
Screenshots
N/A
Desktop (please complete the following information):
- OS: Mac OS 10.15.7 / Windows 10
- Browser any modern browser (Chrome, Safari)
- Version: After migration to http://maayanlab.cloud
[BUG] Pasword reset does not work
Describe the bug
In Password reset
, nothing happens once the email address is entered and the Reset
button is pressed
To Reproduce
Steps to reproduce the behavior:
- Go to 'Login/Password Reset'
- Enter an email and Click on 'Reset'
- Nothing happens
Expected behavior
A feedback is given and an email is sent to the email if it's registered.
Desktop (please complete the following information):
- OS: Win-10
- Browser: Chrome and Firefox
- Version: Current
do enrichr have reactome 2021 as background?
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
- Go to '...'
- Click on '....'
- Scroll down to '....'
- See error
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
library description
Can you please add a description of each library to the website. I found the description in the supplementary data from the 2016 paper but it would be much more useful on the website.
[Question]
Hi,
I have a general question regarding enrichR, it's an useful tools.
hovewer, when performing enrichment analysis, I do not always want to use all gene as background, but a selection of genes (Like gene that are only detected by RNA-seq, or gene that are below a cut off of expression)
My question is so, is it possible to change or to give a list of background gene ?
Thanks in advance and again many thanks for this fabulous tool
Hi, export entries table does not work for me. It exports always the same list of proteins that in addition is not the one that comes out from enrichment. How can I solve this?
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
- Go to '...'
- Click on '....'
- Scroll down to '....'
- See error
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
[BUG]
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
- Go to '...'
- Click on '....'
- Scroll down to '....'
- See error
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
Gene search via the API, how to get structured output
@maxim-k Thank you very much for the answer to my previous issue. I am posting my new question here as I realised that my other issue was closed. Anyway, I have another question about this. I am not that familiar with the json format so I would like to have the output in plaintext, but if I set json=false, I lose the category information. Is it possible to get the output in plaintext but still grouped by category (e.g. Transcription, pathways, etc) and by source (e.g. for Transcription, ChEA 2016, ENCODE and ChEA Consensus TFs from ChIP-X, ARCHS4 TFs Coexp, etc)?
Alternatively, I imagine I could recreate the menu with the categories from the json output, however, not being able to do it myself, is there a script to do it?
Thank you very much in advance
Alfredo
Can't submit fuzzy set to human Enrichr site
I'm trying to submit a fuzzy set to the human Enrichr site, but it doesn't want to take the numbers. It is only giving me to option to submit the gene symbols.
When I paste my list of gene,value into the text box, it converts every row to just the gene when I click submit.
I also tried the enrichr R package and couldn't figure out how to use fuzzy sets.
Here is the list I am trying to submit.
Spp1_top100.txt
An R module for Enrichr
Hi, this is not an issue. I have created an R module for interacting with Enrichr. It can be accessed from here: EnrichR
azimuth library link missing
Describe the bug
The Azimuth library should point to https://azimuth.hubmapconsortium.org/
To Reproduce
Steps to reproduce the behavior:
- Go to 'https://maayanlab.cloud/Enrichr/#libraries'
- See error
Expected behavior
Entry should have hyper link.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
[BUG] YeastEnrichr service not available
Describe the bug
The https://maayanlab.cloud/YeastEnrichr service is not available.
To Reproduce
Steps to reproduce the behavior:
Go to : https://maayanlab.cloud/YeastEnrichr
Desktop (please complete the following information):
- OS: Windows 10
- Browser : Chrome
meaning of combined score
Hi
I love your website it has given me so much insight into my data. Thanks for setting it up.
I was wondering, how is the combined score calculated please? I assume it is a combination of the odds ratio and p value and adjusted p value but can't find any details.
Is there a standard cutoff that people tend to use for combined value (equivalent to the 0.05 people use for p value?)
Thanks again for creating such a useful resource.
best wishes
Rachel
[BUG]
Dear Prof. Ma’ayan,
We decided to export the output of our gene coexpression analysis tool to Enrichr which is an amazing tool that provides numerous enrichment categories, an easy way to import data and comprehensible visualisation of the results.
However, while examining the results, we also noticed some probable discrepancies, which we will try to explain:
- Adjusted p-value calculation.
We have concerns that the False Discovery Rate (FDR) adjusted p-values (visible in the table view of each enrichment category) are incorrect. If we sort the terms with the regular p-values, then the adj p-value of the first ranked term should also be the lowest one. We believe that this is due to the fact that the FDR algorithm wasn't implemented correctly: If a lowest ranked term produces a higher adj p-value than the previous one, then its adj p-value should be equal to the adj p-value of the previous
term.
In order to test this supposition, we used this list of genes as input to Enrichr:
ZPBP
YBX2
PHF7
REXO5
SOX30
We turned our attention to the ARCHS4 TFs Coexp enrichment table. (IMG_1)
The first 8 enrichment terms possess the same p-value, yet their adj p-value is different, which shouldn't be the case.
The pseudocode of FDR algorithm is explained at:
https://riffyn.com/riffyn-blog/2017/10/29/false-discovery-rate
The step which seems to be missing in Enrichr is the following:
"If FDRtemp < FDR Then
FDR = FDRtemp"
In order to test that the method of FDR is correct you can use the following commands in R:
p <- c(.0015,.002,.005, 0.1)
p.adjust(p, method = 'fdr')
[1] 0.004000000 0.004000000 0.006666667 0.100000000
As we can see, the adj p-value results of the two lowest p-value terms (0.0015,0.002) is the same, although the lowest term (0.0015) would produce a higher adj p-value otherwise (pvalue * n/rank, 0.0015*4/1=0.006)
We can only suggest corrections on the adj p-value calculation, since it is the only ranking method we can fully understand.
- Incorrect table header descriptions when mouse hovering.
We have noticed that the description of the table headers is not configured correctly. For example, when mouse hovering over the p-value header in table view, the description for the calculation of the Combined Score is shown instead (IMG_1). We suppose this is due to the fact that the header descriptions were not updated from the previous version of the Enrichr website to the new one.
Furthermore, since we are determined to utilise Enrichr for our research, we would be grateful if a cutoff for each category (P-value, adj P-value, Odds Ratio, Combined Score) could be introduced in the form, for example "Show all results with an adj p-value < 0.05 (user selected number)". We believe it would be a useful addition, helping researchers to ignore non-statistically-significant results.
Thank you in advance.
Yours Sincerely,
Dr Ioannis Michalopoulos - Vasileios Zogopoulos
Just a question: using a bed file as input, what are the rules used to map genes from the genomic coordinates ?
is it the nearest gene or is there a rule like find nearest gene with a maximum distance of +-10kb, etc...
Thanks!!
[QUESTION] Difference Between ChEA2016 and CHEA Transcription Factor Targets Dataset
Describe the bug
These two datasets are very similar. I was wondering exactly what the difference was. I have been told that the later is a better, cleaned up version of ChEA2016.
https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=ChEA_2016 vs. https://maayanlab.cloud/static/hdfs/harmonizome/data/cheappi/gene_attribute_edges.txt.gz
Sources:
https://maayanlab.cloud/Enrichr/#libraries vs. https://maayanlab.cloud/Harmonizome/dataset/CHEA+Transcription+Factor+Targets
Reference for ChEA 2022 datasets
Hello
Can you provide the reference for ChEA 2022?. I need to cite for my poster work
Thank you
File upload feature gone?
Hello!
Today I see that there is no longer the option of uploading a file with gene symbols (instead of copying/pasting it), while a few weeks ago it was possible: will this feature be back at some point?
Thank you and best regards.
can a pathway be uploaded to Enrichr for use?
specifically, the MSigDB Hallmark 2020 Geneset converted to murine orthologs
http://bioinf.wehi.edu.au/software/MSigDB/
publicly available online?
Reactome Library
Hi,
I am curious as to why the Reactome library in Enrichr has not been updated since 2016.
Personally I find this database generally more useful in my work than Kegg for example that you do update.
Thanks
Simon
Table not showing for chem pert library
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
- Go to 'https://maayanlab.cloud/Enrichr/enrich?dataset=8faea06e1ef4175d678ad294bfe83158'
- Click on 'LINCS L1000 Chem Pert down'
- Click on 'Table'
- See error
Expected behavior
Table of results
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: windows
- Browser chrome
- Version [?]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
[BUG] back end failing?
Both the R and web interface failing with multiple error codes:
Lock wait timeout exceeded; try restarting transaction (400)
504 Gateway Time-out
"expired".:true
Tried within work network and on mobile phone data using the example gene-set, as well as a random selection of genes.
As an aside - might be good to have a banner on the website to confirm no planned updates are occuring?
All the best,
Holly
[BUG] Mitochondrial genes are missing in gene ontology analysis
Describe the bug
Thank you for creating EnrichR! I have noticed that when adding human mitochondrial genes they do not generate gene ontologies, for example, GO:0031966. Could you please include the 13 human mitochondrial genes? Such as MT-##? Is there a different gene name than MT-## (## being different for each of the 13 gene names such as MT-CO3)
To Reproduce
Steps to reproduce the behavior:
- Go to 'EnrichR'
- Add mitochondrial gene lists
- No gene ontology information such as cellular component, biological process or molecular function
Expected behavior
A populated Gene ontology list should be available.
Desktop (please complete the following information):
- OS: Windows 10, ubuntu
- Browser chrome
Thanks!!
[BUG]
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
- Go to 'https://maayanlab.cloud/Enrichr/#metadata'
- Click on 'expand a gene'
- enter gene name (APOE for example) the STAT3 example works but not a real gene name from the user....
- Site just rotated the helix symbol and doesn't generate a list
Expected behavior
Generation of a list of co-exressed genes
Desktop (please complete the following information):
- OS: OSX
- Browser ANY
- Version 14.6
Additional context
Add any other context about the problem here.
Gene search via the API, is it possible?
Dear developers,
I would like to use the gene search tool of the Enrichr webserver via the API. Is this possible?
Thanks in advance for your help
Best wishes
Alfredo
[BUG]
Bug description:
The table I export has different values compared with the table displayed on website. example: SUZ12 CHEA combined score was 12.7093 on exported table but 17.45 on table displayed on website. Similar things happened to adjusted p-values and other lines.
Steps to reproduce the behavior:
- Go to EnrichR front page
- Query the gene list
- Click on "ENCODE and ChEA Consensus TFs from ChIP-X"
- Click on "Table"
- "export entries to table"
Expected behavior:
I expected the tables to be the same.
Additonal:
this is the list of queried genes
FBXW5
TTC39A
ACSL1
ECH1
GPT2
CIDEA
FNDC4
PC
PSAT1
SCO1
PPIF
TMEM126A
CSPG5
DHCR7
ULBP3
PTPN3
CNTFR
SLC27A2
ALDH1L1
NDRG4
RETSAT
PEX11A
APCDD1
NPAS4
NACC1
TUBB3
PSMD3
NNAT
SLC16A7
MYH14
PITX3
WLS
NDUFV3
ACSS2
PDE8B
MYH11
STOX1
PCYT1A
NAA50
EGR2
TRAPPC1
SLC35C1
CISH
FIBCD1
SLC30A5
CHCHD10
SLC16A10
PGD
CES4A
ARFGAP2
ACLY
GGCT
SLC6A8
EIF5
PPP1R1B
PPP1R1A
FASN
UBA3
PRR18
PEMT
ATF5
EIF4G2
MT1M
COPB2
LPL
SH3KBP1
FBXO27
MT1X
SLC2A4
TRHDE
SEL1L2
GLIS1
TM7SF2
GLDN
SCGN
LIPE
MPC1
CDH20
APMAP
CPAMD8
FFAR4
GLUL
TXNDC9
C1QTNF1
GYG2
SLC19A3
COX10
PLXNA4
TRMT10A
PRRT4
DUSP4
KCNB1
ATMIN
NAP1L4
WNT9B
SYN2
CYB5A
VEGFA
TF
PTPRF
LPIN1
MAPT
PDE3B
ECHDC3
ACO1
NAT8L
ALK
RTN4
TENM3
RRAD
SAR1B
ABHD5
SHMT1
MRPS11
MCM10
ADIPOR2
AGPAT2
ACACB
ADRA1A
AFF2
HAPLN3
HK2
HEBP2
AACS
RNF157
GHR
FAM83F
ORMDL3
ISOC1
MLX
BOK
SULT4A1
ECEL1
NANOS1
DGAT2
IDH3G
FAM98A
ASCC2
PLEKHG6
PARP1
LGI3
FOS
SLC39A14
HAUS7
TPD52L2
HADHB
FABP5
BDH1
GPAM
GLRB
FOSB
ANGPTL4
USO1
SLC29A2
ANKRD20A8P
TKT
SLC29A4
GCHFR
PNPLA3
USP10
SYCP1
TMEM52
GREB1L
GRAMD4
ACVR1C
FGFRL1
HSD17B10
EPB41L4B
NSDHL
PSMB6
AIFM2
ALDH2
RAC3
NRCAM
ANKRD53
FADS1
PGM1
[BUG] Molecular Function Enrichment doesn't work
Describe the bug
Molecular Function (MF) Enrichment (by using GO_Molecular_Function_2021, GO_Molecular_Function_2020 or GO_Molecular_Function_2019) for both enrichr R package and API doesn't return erichment analysis MF results
for 454 genes sets.
By contrast, the MF enrichment correctly works when I use the enrichr web site with some of the same genes sets.
On the other hand, when I use the test genes set provided by enrichr API guide, it correctly works.
scEnrichr repo missing in GitHub
Git repo listed in scEnrichr appyter page returns a 404.
Is there a new home for scEnrichr description and/or source?
[BUG] genesigdb outdated
Describe the bug
If you perform any enrichment and check results in GeneSIGDB (Disease/Drugs), you can click on table entries to see the original entry. Unfortunately the linked web site is a chinese web site about, well… I don't really know what is about, but definitely not the intended database
could you provide with code of enrichr[BUG]
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:
- Go to '...'
- Click on '....'
- Scroll down to '....'
- See error
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
if I have my own background genes, could you provide us with code to compute p-value and others parameters?
why Reactome have 2016? how to get 2022
https://maayanlab.cloud/Enrichr/
Add SynGO to enrichR databases
Hi,
Would it be possible to add SynGO https://www.syngoportal.org/ to the list of databases to check for enrichment?
Thanks
Is it possible to know if all gene names are recognized?
Sometimes, there is inconsistency in gene names. One gene may have several names. Is there anyway to know if Enrichr recognize all gene names in the input gene list? Mis-recognition may lead to false positive or false negative results. Thanks!
[BUG] Set custom background?
Fantastic GO enrichment tool!
Wondering if the option to set your own custom background has been implemented or if there are plans to?
Thanks!
Terms and genes seem to be missing
I have a gene set of 404 mouse genes (https://gist.github.com/jackh726/3296f36b1d06245d8b741ef1a5151663).
When I run this set through Panther with "GO Biological Process", one term that pops up is "lung development" (GO:0030324), with 26/216 genes found. Similarly, running the set through ShinyGO gives lung development as a top-enriched term (23/210 genes found). However, running through Enrichr has an insignficant adjusted p-value, with only 4 genes matching. Indeed, when I did a term search (https://maayanlab.cloud/Enrichr/#meta!meta=lung%20development) and downloaded the gene set, there are only 35.
To make things even more confusing, the highest fold-enrichment term in Panther (astrocyte activation involved in immune response) doesn't show up in the term search for Enrichr at all.
Looking up the ontology term does show ~230 genes for mouse (http://amigo.geneontology.org/amigo/search/bioentity?q=*:*&fq=isa_partof_closure:%22GO:0030324%22&fq=taxon_subset_closure_label:%22Mus%20musculus%22&sfq=document_category:%22bioentity%22), which is close to what Panther and ShinyGO show, and very different from what is shown with Enrichr.
Possibility of doing enrichment analysis based on a list of isoforms
Is it possible to do the enrichment analysis based on a set of isoform IDs?
Export function
Hello,
There seems to be an issue with the " Export entries to table" function from the web, as below:
{
"expired": true
}
It's also affecting the R-package enrichR dependent on it.
> genelist<-c(c("KRAS", "NF1", "APC"))
> dbs<-c("WikiPathways_2019_Human")
> library(enrichR)
> enrichr(genelist,dbs)
Uploading data to Enrichr... Done.
Querying WikiPathways_2019_Human... Done.
Parsing results... Done.
$WikiPathways_2019_Human
X.
1 "expired": true
2 }
I guess it's temporary as you guys are updating the tool?
Thanks a lot!
Nick
[BUG] Different gmt files are used in Enrichr server and download package
It is originally reported to zqfang/GSEApy#122.
However, it seems to me that the root cause of the issue is probably because the gmt files that we can download from https://maayanlab.cloud/Enrichr/#stats are different from those used in the Enrichr server.
[BUG]
Describe the bug
Password reset does not work.
To Reproduce
Steps to reproduce the behavior:
- Go to https://maayanlab.cloud/Enrichr/login.html
- Click on Password reset
- Enter email address
- Click Reset
- Nothing happens in both Chrome and Safari
Expected behavior
Password is reset/email with reset instructions sent.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: macOS Mojave 10.14.6
- Browser: Chrome and Safari
- Version: Latest for both
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
Documentation does not describe how bed file is converted to gene
presumably is is some version of closest promoter - but it is not made clear AFAICS
BED file input capability - September 9th, 2014
Enrichr can now accept BED files as input for enrichment. Enrichr automatically converts the BED file into a gene list. The species supported are human and mouse. The maximum number of genes to produce from the bed file can be adjusted. If the gene list produced by the conversion has more genes than the maximum, Enrichr will take the best matching 500, 1000 or 2000 genes. The file must have the extension ".bed" and must be uploaded, not copy and pasted.
Change descriptive text to LGI3" is down-regulated in a signature created from "
Describe the bug
Change descriptive text to LGI3" is down-regulated in a signature created from "
To Reproduce
Steps to reproduce the behavior:
- Go to 'Gene Search'
- Type in LGI3
- Scroll down to "RNAseq Automatic GEO Signatures Human Down"
- See TEXT that needs to be fixed (also fix the Up and for human and mouse)
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
HuBMAP_ASCT_plus_B_augmented_w_RNAseq_Coexpression Dataset Preparation Details
Can you provide some details on the preparation of the cell type gene sets in the HuBMAP_ASCT_plus_B_augmented_w_RNAseq_Coexpression Dataset. This would be very helpful for understanding the use of some markers for different cell types.
Thanks very much.
[BUG]enrichR not working
Describe the bug
A clear and concise description of what the bug is.
The R package enrichr function not working
To Reproduce
the library loading and function calling function both showed database not responding while the web interface works well
Expected behavior
Working enrichR function
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
MacOS
enrichR 3.0
Additional context
Add any other context about the problem here.
[BUG]
Describe the bug
When trying to access the appyter figures I am unable to establish a secure connection to the server. Have tried on multiple devices/web browsers
Desktop:
- Browser [ chrome, safari and firefox]
is it possible to search all libraries together via the API
The only examples on the https://maayanlab.cloud/Enrichr/help#api page involve doing enrichment analysis on only a single gene set library. Of course it's possible to loop over the libraries one at a time but this is orders of magnitude less efficient than the performance one gets with through the browser interface, so it doesn't seem great.
Is there a way to specify multiple libraries in the API? Or is there a nice example of how to download all the libraries and run the enrichment offline?
Thanks.
Links from library pages are all broken
Describe the bug
Links from library pages are all broken
To Reproduce
Steps to reproduce the behavior:
- Go to 'https://maayanlab.cloud/Enrichr/#libraries'
- Click on 'any library label'
- See error
Expected behavior
Link should lead to the source
Desktop (please complete the following information):
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]
Smartphone (please complete the following information):
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]
Additional context
Add any other context about the problem here.
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