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318 results • Page 1 of 7
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1
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0
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115
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Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
1 day ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
188
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
13 days ago by rohitsatyam102 ▴ 780
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 weeks ago by ▴ 50 • written 3.3 years ago by ▴ 160
0
votes
0
replies
266
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
4 weeks ago by rohitsatyam102 ▴ 780
0
votes
4
replies
466
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
27 days ago by Coremine Medical ▴ 20
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 5 weeks ago by 41k • written 10.1 years ago by ★ 7.8k
48
votes
30
replies
9.4k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 5 weeks ago by 78k • written 7.8 years ago by 41k
1
vote
0
replies
296
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
5 weeks ago by Ming Tommy Tang ★ 3.6k
10
votes
31
replies
10.0k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 weeks ago by • 0 • written 5.9 years ago by ▴ 320
2
votes
0
replies
373
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 12 weeks ago by 41k • written 12 weeks ago by 158k
0
votes
1
reply
330
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 12 weeks ago by 78k • written 12 weeks ago by ▴ 30
4
votes
2
replies
2.5k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 3 months ago by 136k • written 3.6 years ago by 78k
0
votes
0
replies
437
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
3 months ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
382
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
3 months ago by Ming Tommy Tang ★ 3.6k
13
votes
3
replies
14k
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 3 months ago by ▴ 20 • written 6.7 years ago by ★ 1.6k
5
votes
2
replies
723
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 3 months ago by 41k • written 3 months ago by ★ 2.4k
0
votes
0
replies
334
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
3 months ago by Ming Tommy Tang ★ 3.6k
9
votes
4
replies
4.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
4 months ago by Hamid Ghaedi 3.1k
6
votes
0
replies
369
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
3 months ago by barslmn ★ 2.0k
0
votes
0
replies
538
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
4 months ago by Starlitnightly • 0
1
vote
0
replies
434
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 4 months ago by 41k • written 4 months ago by ★ 3.6k
3
votes
1
reply
452
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 4 months ago by 41k • written 4 months ago by 8.4k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
1
vote
0
replies
478
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 4 months ago by 41k • written 4 months ago by ★ 3.6k
0
votes
0
replies
676
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
4 months ago by Starlitnightly • 0
19
votes
13
replies
8.0k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 weeks ago by • 0 • written 17 months ago by 78k
2
votes
0
replies
2.9k
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 4 months ago by 41k • written 4 months ago by ★ 3.6k
19
votes
7
replies
6.1k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 4 months ago by 78k • written 3.7 years ago by 5.8k
3
votes
2
replies
676
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
4 months ago by Ming Tommy Tang ★ 3.6k
88
votes
22
replies
84k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 months ago by • 0 • written 5.4 years ago by ▴ 580
2
votes
0
replies
340
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
4
votes
0
replies
548
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
5 months ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
453
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
0
votes
0
replies
459
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
5 months ago by sinha.shriprakash ▴ 20
1
vote
2
replies
638
views
Tutorial: How to ask computational biology questions
computational-biology
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
1
vote
0
replies
482
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 5 months ago by 41k • written 5 months ago by ★ 3.6k
2
votes
0
replies
526
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
5 months ago by Ming Tommy Tang ★ 3.6k
1
vote
0
replies
477
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
5 months ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
521
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
6 months ago by Coremine Medical ▴ 20
2
votes
0
replies
528
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 6 months ago by 41k • written 6 months ago by ▴ 20
3
votes
0
replies
790
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
7 months ago by Ming Tommy Tang ★ 3.6k
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 7 months ago by 136k • written 10.0 years ago by 20k
2
votes
0
replies
869
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 8 months ago by 78k • written 8 months ago by ▴ 40
1
vote
0
replies
607
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 4 weeks ago by 41k • written 8 months ago by ▴ 10
3
votes
2
replies
2.5k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
7
votes
3
replies
2.0k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 8 months ago by ▴ 110 • written 16 months ago by 86k
3
votes
3
replies
2.5k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 9 months ago by 41k • written 20 months ago by ★ 3.3k
2
votes
0
replies
959
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 24 days ago by • 0 • written 10 months ago by ★ 1.6k
11
votes
7
replies
1.9k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 months ago by barslmn ★ 2.0k
2
votes
1
reply
1.9k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 11 months ago by 158k • written 11 months ago by ★ 2.0k
318 results • Page 1 of 7
Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
Answer: Read count vs Depth
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Recent Awards • All
Scholar to Trivas ★ 1.5k
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Recent Replies
Comment: Genetic data QC prior to imputation by Raony Guimarães ★ 1.3k
Check how many variants you have without filtering for MAF, maybe use a MAF of 0.01? You could try the --impute-sex **ycount** or **y-only*…
Comment: Differential expression using Bowtie2 by ATpoint 78k
> What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq data? Get a dataset that has ev…
Comment: How to query 1000 genomes project VCF files for specific regions without downloa by kilojarek ▴ 10
Thanks @Pierre this is great to know, although it doesn't solve my issue of this being R-self-contained. rsamtools doesn't seem to carry fu…
Comment: Differential expression using Bowtie2 by 8d8fc19e • 0
Ok, thanks for letting me know. What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq da…
Comment: SQL request from NCBI metadata and stat_analysis tables by marie.harmel • 0
To put it more simply with another example, I try to display every possible order for every phyla founded in my run but I don't find the l…
Comment: SQL request from NCBI metadata and stat_analysis tables by marie.harmel • 0
Thank you for your answer but unfortunately I tried it and it makes the same kind of ouptut as mine, with multtiple new (false) lines (spl…
Comment: Normalization of RNA captureSeq data (<20 genes captured) by ATpoint 78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen by j.gleixner • 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci by GenoMax 136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci by Pierre Lindenbaum 158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline by ju_ra • 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms? by Elisabeth Gasteiger ★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by Pierre Lindenbaum 158k
again, it's a problem with the variant caller, which is ?
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