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323 results • Page 1 of 7
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Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 15 days ago by 40k • written 15 days ago by 157k
0
votes
1
reply
184
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 16 days ago by 77k • written 16 days ago by ▴ 30
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 23 days ago by 134k • written 3.4 years ago by 77k
0
votes
0
replies
243
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
5 weeks ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
230
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
5 weeks ago by Ming Tommy Tang ★ 3.4k
13
votes
3
replies
11k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
5
votes
2
replies
448
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 6 weeks ago by 40k • written 6 weeks ago by ★ 2.4k
0
votes
0
replies
191
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
6 weeks ago by Ming Tommy Tang ★ 3.4k
9
votes
4
replies
4.0k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
7 weeks ago by Hamid Ghaedi 3.0k
6
votes
0
replies
219
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
6 weeks ago by barslmn ★ 1.8k
0
votes
0
replies
238
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
7 weeks ago by Starlitnightly • 0
1
vote
0
replies
289
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 8 weeks ago by 40k • written 8 weeks ago by ★ 3.4k
3
votes
1
reply
314
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 8 weeks ago by 40k • written 8 weeks ago by 8.2k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 weeks ago by • 0 • written 7.6 years ago by 20k
1
vote
0
replies
315
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 10 weeks ago by 40k • written 10 weeks ago by ★ 3.4k
0
votes
0
replies
428
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
10 weeks ago by Starlitnightly • 0
18
votes
13
replies
6.8k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 10 weeks ago by 53k • written 15 months ago by 77k
2
votes
0
replies
2.7k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 11 weeks ago by 40k • written 11 weeks ago by ★ 3.4k
18
votes
7
replies
5.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 weeks ago by 77k • written 3.5 years ago by 5.5k
3
votes
2
replies
468
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
10 weeks ago by Ming Tommy Tang ★ 3.4k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 11 weeks ago by • 0 • written 5.2 years ago by ▴ 580
2
votes
0
replies
233
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 11 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
4
votes
0
replies
353
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
3 months ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
277
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 3 months ago by 40k • written 3 months ago by ★ 3.4k
0
votes
0
replies
300
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
3 months ago by sinha.shriprakash ▴ 20
1
vote
2
replies
475
views
Tutorial: How to ask computational biology questions
computational-biology
updated 3 months ago by 40k • written 3 months ago by ★ 3.4k
1
vote
0
replies
346
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 3 months ago by 40k • written 3 months ago by ★ 3.4k
2
votes
0
replies
330
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
3 months ago by Ming Tommy Tang ★ 3.4k
1
vote
0
replies
350
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
3 months ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
389
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
3 months ago by Coremine Medical ▴ 10
1
vote
0
replies
366
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 3 months ago by 40k • written 3 months ago by ▴ 10
3
votes
0
replies
659
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
4 months ago by Ming Tommy Tang ★ 3.4k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 months ago by 134k • written 9.9 years ago by 20k
2
votes
0
replies
729
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 6 months ago by 77k • written 6 months ago by ▴ 40
1
vote
0
replies
464
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
6 months ago by Milad ▴ 10
3
votes
2
replies
2.4k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 4 months ago by 40k • written 6.4 years ago by ▴ 100
7
votes
3
replies
1.7k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 5 months ago by ▴ 110 • written 13 months ago by 86k
3
votes
3
replies
2.2k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 7 months ago by 40k • written 17 months ago by ★ 3.3k
1
vote
0
replies
727
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
8 months ago by firestar ★ 1.6k
11
votes
7
replies
1.7k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
6 months ago by barslmn ★ 1.8k
2
votes
1
reply
1.5k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 8 months ago by 157k • written 8 months ago by ★ 1.8k
3
votes
2
replies
1.6k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
10 weeks ago by Dr.Animo ▴ 60
2
votes
0
replies
850
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 3 months ago by 40k • written 9 months ago by ▴ 360
1
vote
0
replies
2.1k
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 3 months ago by 40k • written 9 months ago by ▴ 360
5
votes
0
replies
958
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 3 months ago by 40k • written 9 months ago by ▴ 360
6
votes
0
replies
2.5k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
7 months ago by Novogene ▴ 360
50
votes
1
reply
7.4k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 7 months ago by 40k • written 3.0 years ago by 77k
1
vote
3
replies
690
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
6 months ago by barslmn ★ 1.8k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.1 years ago by 86k
13
votes
31
replies
5.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 6 months ago by 40k • written 4.1 years ago by 8.2k
323 results • Page 1 of 7
Recent Votes
A: Individual VCF files from main VCF file
Individual VCF files from main VCF file
A: Splitting vcf files to individual samples
Splitting vcf files to individual samples
Answer: Chip-Seq and correlation of bam file
Comment: Chip-Seq and correlation of bam file
BWA mem bam output name sorted
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Scholar to rfran010 ▴ 830
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Recent Replies
Comment: Unmapped Reads in Kallisto by dsull ★ 4.7k
Sounds good! I just added a solution here.
Answer: Unmapped Reads in Kallisto by dsull ★ 4.7k
Running kallisto bus with the -n option will record the read numbers of the reads that have been successfully mapped in the output BUS file…
Comment: Automate the Splitting of a VCF File by Sample (bcftools) by cfos4698 ▴ 830
Just a comment re: your bash example reading from a file. Have you tried `while` instead of 'with'? ``` while read sample; do bcftools…
Comment: Split plink files by a number of SNPs by Raygozak ★ 1.4k
Out of curiosity, why would someone ask how to do something if they already knew how to do it or which tools to use? Also, the OP is not a…
Comment: Comparing multiple RNASeq studies by Zhenyu Zhang ▴ 980
no. The best you can do is to draw conclusion using one dataset, and validate your conclusion using other datasets.
Comment: comparision of umap single cell by synat.keam ▴ 80
Thank, Seniors.. I figured out the issue of my integration as I did not state the ``` reduction= "harmony" ```
Comment: Issue with merging in plink and eigensoft. by bk11 ★ 1.2k
> I merged two datasets in plink1.9. It worked, but I did get the error > "multiple positions seen for variant" and "variants have the same…
Comment: How to subset large BAM files specifically/ extract specific subsets? by ella • 0
It worked now, after re-mapping with short-headed FASTA! :) Thanks a lot again for your time.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data by svlachavas ▴ 780
Dear LChart, thanks a million for your detailed response and explanations !! Some quick updated comments (hopefully not disturb you furth…
Comment: Clustering in single cell by Chris ▴ 200
Just because the articles and tutorials I read, they usually clearly separate which I worry I did something wrong.
Comment: How to subset large BAM files specifically/ extract specific subsets? by GenoMax 134k
> do you think the one or other option (using fasta with shortened > headers vs. bbmap.sh with trd=t option) would have other advantages or…
Comment: Clustering in single cell by bk11 ★ 1.2k
> However, in my analysis, clusters of each cell types are not clearly > separate even though I tried different clustering algorithms (louv…
Comment: How to subset large BAM files specifically/ extract specific subsets? by ella • 0
I think I even used `reformat.sh` earlier today, but don´t remember with what arguments. I now tried what you suggested, but got an error: …
Comment: Clustering in single cell by Jean-Karim Heriche 26k
Are you doing the clustering in UMAP space? If so, avoid distance-based clustering because distances are only meaningful locally, i.e dista…
Comment: Github access with token headache by Ram 40k
Yes please.
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