Commit c15f7b94 authored by Mikaël Salson's avatar Mikaël Salson
Browse files

doc/: Fix broken URLs

parent c5cfd578
......@@ -90,44 +90,44 @@ BMC Genomics 2014, 15:409
Jean-Sebastien Allain et al.,
*IGHV segment utilization in immunoglobulin gene rearrangement differentiates patients with anti-myelin-associated glycoprotein neuropathy from others immunoglobulin M-gammopathies*,
Haematologica, 2018, 103:e207-e210
<http://dx.doi.org/10.3324/haematol.2017.177444>
http://dx.doi.org/10.3324/haematol.2017.177444
Yann Ferret et al.,
*Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis*,
British Journal of Haematology, 2016, 173, 413–420
<http://dx.doi.org/10.1111/bjh.13981>
http://dx.doi.org/10.1111/bjh.13981
Henrike J. Fischer et al.,
*Modulation of CNS autoimmune responses by CD8+ T cells coincides with their oligoclonal expansion*
Journal of Neuroimmunology, 2015, S0165-5728(15)30065-5
<http://dx.doi.org/10.1016/j.jneuroim.2015.10.020>
http://dx.doi.org/10.1016/j.jneuroim.2015.10.020
Michaela Kotrova et al.,
*The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL*,
Blood, 2015, 126:1045-1047
<http://dx.doi.org/10.1182/blood-2015-07-655159>
http://dx.doi.org/10.1182/blood-2015-07-655159
Michaela Kotrova et al.,
*Next‐generation amplicon TRB locus sequencing can overcome limitations of flow‐cytometric Vβ expression analysis and confirms clonality in all T‐cell prolymphocytic leukemia cases*,
Cytometry Part A, 93(11):1118-1124, 2018
<http://dx.doi.org/10.1002/cyto.a.23604>
http://dx.doi.org/10.1002/cyto.a.23604
Ralf A. Linker et al.,
*Thymocyte-derived BDNF influences T-cell maturation at the DN3/DN4 transition stage*
European Journal of Immunology, 2015, 45, 1326-1338
<http://dx.doi.org/10.1002/eji.201444985>
http://dx.doi.org/10.1002/eji.201444985
Mikaël Salson et al.,
*High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones*,
Leukemia Research, 2017, 53, 1–7
<http://dx.doi.org/10.1016/j.leukres.2016.11.009>
http://dx.doi.org/10.1016/j.leukres.2016.11.009
Florian Scherer et al.,
*Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA*,
Science Translational Medicine, 2016, 8, 364ra155
<http://dx.doi.org/10.1126/scitranslmed.aai8545>
http://dx.doi.org/10.1126/scitranslmed.aai8545
Edit Porpaczy et al.,
*Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy*,
Blood, 2018,
<https://dx.doi.org/10.1182/blood-2017-10-810739>
https://dx.doi.org/10.1182/blood-2017-10-810739
......@@ -200,7 +200,7 @@ Then `docker ps` should display five running containers:
- Copy also the generated `browser/js/germline.js` into the `docker/vidjil-client/conf/` directory.
- Open a web browser to <https://localhost>, or to your FQDN if you configured it (see above).
- Open a web browser to `https://localhost`, or to your FQDN if you configured it (see above).
Click on `init database` and create a first account by entering an email.
This account is the main root account of the server. Other administrators could then be created.
It will be also the web2py admin password.
......@@ -363,7 +363,7 @@ docker load -i <input_file>
In some cases, you may need to update your `docker-compose.yml` file or some
of the configuration files. We will describe the changes in the `CHANGELOG` file.
The latest versions of these files are available on our
[Gitlab](https://gitlab.vidjil.org/).
[Gitlab](http://gitlab.vidjil.org/).
Once the images are pulled, you can relaunch the containers:
```sh
......
......@@ -5,7 +5,7 @@ Vidjil is an open-source platform for the analysis of high-throughput sequencing
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
High-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html) methods and software.
This is the help of the [Vidjil web application](http://app.vidjil.org/browser/).
This is the help of the [Vidjil web application](http://app.vidjil.org/).
Further help can always be asked to <support@vidjil.org>. We can also arrange phone or video meeting.
The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
......
......@@ -669,7 +669,7 @@ Using `-c designations` trigger a separate analysis for each read, but this is u
| duplicate_count | number | Number of reads contributing to the (UMI) consensus for this sequence. For example, the sum of the number of reads for all UMIs that contribute to the query sequence. <br />*Number of reads gathered in the clone.*
| sequence_id | string | Unique query sequence identifier within the file. Most often this will be the input sequence header or a substring thereof, but may also be a custom identifier defined by the tool in cases where query sequences have been combined in some fashion prior to alignment. <br />*This identifier is the (50 bp by default) window extacted around the junction.* |
| clone_id | string | Clonal cluster assignment for the query sequence. <br />*This identifier is again the (50 bp by default) window extacted around the junction.*
| warnings (+) | string | *Warnings associated to this clone. See <https://gitlab.vidjil.org/blob/dev/doc/warnings.md>.*
| warnings (+) | string | *Warnings associated to this clone. See <http://gitlab.vidjil.org/blob/dev/doc/warnings.md>.*
| sequence | string | The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment. <br />*This contains the consensus/representative sequence of each clone.*
| rev_comp | boolean | True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'. <br />*Set to null, as vidjil-algo gather reads from both strands in clones* |
| v_call, d_call, j_call | string | V/D/J gene with allele. For example, IGHV4-59\*01. <br /> *implemented. In the case of uncomplete/unexpected recombinations (locus with a `+`), we still use `v/d/j_call`. Note that this value can be null on clones beyond the `--max-designations` option.* |
......
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