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143 results • Page 2 of 3
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20
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2
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8.1k
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Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.4k
1
vote
2
replies
873
views
Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 11 months ago by 43k • written 7.0 years ago by 27k
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.7 years ago by ▴ 90
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
3
votes
2
replies
528
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 3 months ago by ▴ 120
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 11 months ago by 43k • written 7.0 years ago by ▴ 30
5
votes
2
replies
3.1k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 11 months ago by 43k • written 7.0 years ago by ★ 9.4k
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 months ago by Ming Tommy Tang ★ 3.9k
6
votes
2
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by GenoMax 141k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 4.0 years ago by 82k
0
votes
1
reply
97
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 2 hours ago by 43k • written 19 hours ago by ★ 3.9k
1
vote
1
reply
323
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
1
reply
3.4k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 11 weeks ago by ▴ 120 • written 2.7 years ago by 87k
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 11 months ago by 43k • written 6.7 years ago by ▴ 40
0
votes
1
reply
535
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
1
reply
638
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.5k
10
votes
1
reply
9.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by 43k • written 6.6 years ago by ▴ 110
2
votes
1
reply
402
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
7
votes
1
reply
2.2k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 11 months ago by 43k • written 6.5 years ago by ★ 1.7k
0
votes
1
reply
526
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 7 months ago by 82k • written 7 months ago by ▴ 30
0
votes
1
reply
286
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 3 months ago by ▴ 120
6
votes
1
reply
431
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
1
reply
3.2k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 11 months ago by 43k • written 6.5 years ago by • 0
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
15
votes
1
reply
7.1k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.0k
1
vote
0
replies
1.4k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.3 years ago by ▴ 90
7
votes
0
replies
592
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
1
vote
0
replies
682
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
replies
310
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
3 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
335
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
3.6k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
1
vote
0
replies
320
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
1.6k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
0
votes
0
replies
244
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
269
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
1.7k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 11 months ago by 43k • written 6.7 years ago by ▴ 350
0
votes
0
replies
307
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
252
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
0
replies
200
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
8 weeks ago by Novogene ▴ 420
1
vote
0
replies
629
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 8 months ago by 43k • written 8 months ago by ★ 3.9k
4
votes
0
replies
767
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
648
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
10 months ago by sinha.shriprakash ▴ 20
2
votes
0
replies
707
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 10 months ago by 43k • written 10 months ago by ▴ 20
4
votes
0
replies
951
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
11 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
1.6k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
1
vote
0
replies
2.6k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 10 months ago by 43k • written 16 months ago by ▴ 420
0
votes
0
replies
672
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
8 months ago by Ming Tommy Tang ★ 3.9k
143 results • Page 2 of 3
Recent Votes
Comment: Sequence read length shorter than flow cell specification
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
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Recent Replies
Answer: Sequence read length shorter than flow cell specification by swbarnes2 14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
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