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Showing top results for tag: TCR • reset
13
votes
23
replies
16k
views
11 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 6 weeks ago by • 0 • written 5.4 years ago by ★ 18k
0
votes
1
reply
456
views
10x VDJ (TCR/BCR) BAM to fastq
TCR VDJ BCR 10x
updated 6 months ago by 146k • written 6 months ago by ★ 2.0k
1
vote
5
replies
2.8k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 6 months ago by 85k • written 5.6 years ago by ▴ 750
0
votes
0
replies
264
views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
Annotation TCR Epitope-specificity
8 months ago by tim • 0
1
vote
2
replies
662
views
TCR target prediction
TCR genomics sequencing seurat 10x repertoire scRNA
updated 8 months ago by 44k • written 2.5 years ago by ▴ 10
2
votes
5
replies
4.2k
views
Any tools for predicting binding affinity between TCR and epitode?
prediction TCR cancer
updated 8 months ago by • 0 • written 6.4 years ago by ▴ 750
2
votes
1
reply
546
views
Interpretation of output from MiXCR TCR sequencing
MiXCR TCR sequencing
updated 10 months ago by 14k • written 10 months ago by • 0
0
votes
0
replies
781
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
14 months ago by Ming Tommy Tang ★ 4.4k
4
votes
6
replies
2.8k
views
How to add VDJ clonotyping data to Seurat object of scRNA-seq
scRNA-seq 10x single-cell TCR
16 months ago by Akira ▴ 10
0
votes
2
replies
776
views
BCR/TCR analysis using target capture sequencing data
capture ngs TCR BCR
17 months ago by J.F.Jiang ▴ 930
1
vote
2
replies
901
views
How to infer CDR1, CDR2, and CDR3 sequences from a TCR chain protein sequence?
TCR CDR2 CDR3 VDJ CDR1
18 months ago by nomorewords • 0
4
votes
4
replies
1.7k
views
How to do typing of VDJ regions for10x TCR kit?
TCRA Immunology TCR
updated 21 months ago by ▴ 60 • written 2.2 years ago by ▴ 70
1
vote
4
replies
1.2k
views
filter out T cell clones
vdjtools TCR mixcr
updated 16 months ago by 44k • written 23 months ago by ▴ 40
6
votes
4
replies
2.3k
views
Help and idea with TCR/BCR analysis
BCR TCR scRNA-seq
updated 21 months ago by ▴ 60 • written 2.0 years ago by ★ 4.3k
0
votes
1
reply
967
views
Comparing 5'RACE TCR Sequencing Methods
TCR 5'RACE repertoire MiXCR clones
updated 21 months ago by ▴ 60 • written 4.4 years ago by ▴ 40
0
votes
2
replies
2.4k
views
TCR data analysis
next-gen TCR
updated 21 months ago by ▴ 60 • written 5.7 years ago by • 0
1
vote
1
reply
816
views
Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq)
umitools single-cell mixcr seurat tcr
updated 16 months ago by 44k • written 2.7 years ago by ▴ 230
0
votes
1
reply
998
views
Low alignment rates for randomly shredded TCR-B library with MixCR
alignment shotgun MixCR TCR
updated 21 months ago by ▴ 60 • written 2.7 years ago by ▴ 140
0
votes
1
reply
824
views
mixcr targetQualities
repertoire mixcr tcr
updated 21 months ago by ▴ 60 • written 3.1 years ago by ▴ 10
0
votes
2
replies
685
views
Human cell atlas TCR analysis
TCR cell single
2.1 years ago by datanerd ▴ 520
0
votes
0
replies
397
views
TCR data from HCA and ImmuneCode
TCR
2.1 years ago by datanerd ▴ 520
0
votes
1
reply
1.3k
views
GLIPH version 2 question
RNA-Seq R GLIPH TCR 10X
updated 2.5 years ago by ▴ 20 • written 3.8 years ago by ▴ 60
0
votes
1
reply
635
views
Assigning V, D, J and C to nanopore sequence
nanopore repertoire annotation sequence TCR
updated 2.8 years ago by 6.8k • written 2.8 years ago by ▴ 160
2
votes
6
replies
1.6k
views
Map TCR sequences from bulk mRNA seq
tcr
updated 2.4 years ago by 44k • written 2.8 years ago by ▴ 40
0
votes
2
replies
1.2k
views
Cluster mouse single CD4 T cells according to TCR seq data
TCR
2.9 years ago by chi.delta ▴ 40
1
vote
1
reply
1.2k
views
Corelate TCR data to clusters/GEX/CITEseq data
10x vdj tcr seurat
updated 3.2 years ago by ▴ 240 • written 3.4 years ago by ▴ 40
1
vote
1
reply
1.1k
views
Analyzing TCRseq Data
tcr TCRseq scRepetoire Immunarch
updated 3.2 years ago by ▴ 240 • written 3.7 years ago by ▴ 80
0
votes
0
replies
741
views
Gini Index Box plot
RNA-Seq TCR R Seurat 10x
3.3 years ago by roberts ▴ 60
9
votes
4
replies
4.7k
views
TCR RNAseq Single Cell Data Analysis
TCR ImmunoSeq RNA-Seq Single Cell Paired
updated 7.3 years ago by • 0 • written 8.0 years ago by ▴ 260
2
votes
3
replies
1.2k
views
Differential abundance analysis for bulk TCR-seq data
enrichment TCR differential DESEQ
3.5 years ago by pm2012 ▴ 140
0
votes
1
reply
1.3k
views
FASTQ level UMI correction for TCR analysis
UMI fastq TCR RNA-Seq Mixcr
3.7 years ago by gordo2b ▴ 10
2
votes
14
replies
2.9k
views
TCR analysis in Suerat
RNA-Seq R Seurat TCR 10X
updated 4.1 years ago by ★ 18k • written 4.1 years ago by ▴ 60
0
votes
0
replies
836
views
pulling out TCR data
Seurat R TCR RNA-Seq VDJ
4.1 years ago by roberts ▴ 60
1
vote
2
replies
4.7k
views
Analyzing TCR clonotype in Seurat
RNA-Seq R Seurat 10x TCR
updated 4.1 years ago by ★ 18k • written 4.1 years ago by ▴ 60
2
votes
0
replies
1.7k
views
Tool: Fast and painless exploration of single-cell/bulk T-cell and antibody repertoires in R
repseq antibody immunology airr tcr
updated 16 months ago by 44k • written 4.4 years ago by ▴ 90
0
votes
1
reply
1.7k
views
scRNAseq T cell receptor clonotype analysis - some cells missing alpha or beta chain sequence? Need advice
thymocyte TCR T cell receptor clonotype 10X
updated 5.3 years ago by 20 • written 5.3 years ago by ▴ 10
0
votes
0
replies
853
views
Why seed and fuzzy-search in MIGEC?
MIGEC MUI tcr
5.5 years ago by CY ▴ 750
1
vote
1
reply
1.4k
views
Capturing TCR from cfDNA
TCR cfDNA ctDNA
5.6 years ago by CY ▴ 750
4
votes
1
reply
2.0k
views
Adaptive T cell receptor productive clone missing
TCR sequencing Adaptive Productive Clone
updated 5.8 years ago by 20 • written 8.0 years ago by ▴ 260
7
votes
25
replies
11k
views
6 follow
Tool: MIGEC: towards error-free profiling of immune repertoires
sequencing-error tcr antibody molecular-barcode
updated 16 months ago by 44k • written 10.5 years ago by 3.5k
0
votes
1
reply
1.8k
views
Takara Mouse TCR a/b Profiling Sample Multiplexing
RNA-Seq TCR Takara
6.9 years ago by bioinformatics.cancer ▴ 260
12
votes
1
reply
5.2k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 2.1 years ago by 44k • written 9.2 years ago by 3.5k
6
votes
16
replies
7.5k
views
6 follow
Forum: Immune repertoire sequencing community
sequencing repseq immunology tcr ig
updated 2.7 years ago by 44k • written 10.2 years ago by 3.5k
6
votes
12
replies
3.0k
views
TCR Sequencing Lack of Repertoire Overlap
TCR Sequencing Repertoire
updated 8.4 years ago by 20k • written 8.4 years ago by ▴ 260
4
votes
2
replies
3.1k
views
Cancer TCR Repertoire Datasets
sequence Cancer TCR Repertoire Dataset
updated 8.4 years ago by 3.5k • written 8.4 years ago by ▴ 260
4
votes
2
replies
3.8k
views
T Cell CDR3 sequence database
CDR3 Anitgen Database Sequence TCR
updated 8.6 years ago by 3.5k • written 8.6 years ago by ▴ 260
46 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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