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143 results • Page 2 of 3
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14
votes
3
replies
20k
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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 8 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
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
1
vote
0
replies
534
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
8 months ago by Ming Tommy Tang ★ 3.9k
9
votes
4
replies
5.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months ago by Hamid Ghaedi 3.2k
7
votes
0
replies
595
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
1
vote
0
replies
635
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
3
votes
1
reply
645
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
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 months ago by • 0 • written 8.1 years ago by 20k
1
vote
0
replies
684
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
21
votes
13
replies
10k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 months ago by • 0 • written 22 months ago by 82k
2
votes
0
replies
3.2k
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 9 months ago by 43k • written 9 months ago by ★ 3.9k
19
votes
7
replies
6.6k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 months ago by 82k • written 4.1 years ago by 6.4k
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
93
votes
23
replies
92k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by • 0 • written 5.8 years ago by ▴ 610
2
votes
0
replies
474
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
4
votes
0
replies
775
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
665
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
replies
651
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
1
vote
2
replies
880
views
Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
684
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
3
votes
0
replies
738
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
10 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
608
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
670
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
10 months ago by Coremine Medical ▴ 20
2
votes
0
replies
711
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
953
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
12 months ago by Ming Tommy Tang ★ 3.9k
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 12 months ago by 141k • written 10.4 years ago by 20k
1
vote
0
replies
817
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 5 months ago by 43k • written 13 months ago by ▴ 10
3
votes
2
replies
2.7k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 5 months ago by • 0 • written 15 months ago by ★ 1.6k
2
votes
0
replies
1.2k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 10 months ago by 43k • written 16 months ago by ▴ 420
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
5
votes
0
replies
1.6k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 10 months ago by 43k • written 16 months ago by ▴ 420
1
vote
2
replies
1.5k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 10 months ago by 43k • written 19 months ago by ▴ 20
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.2 years ago by ▴ 420
83
votes
34
replies
19k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 months ago by • 0 • written 5.9 years ago by ★ 1.3k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 10 months ago by 43k • written 5.2 years ago by ▴ 170
149
votes
70
replies
50k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 8 months ago by ▴ 260 • written 6.4 years ago by 87k
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
99
votes
106
replies
46k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 20 days ago by ▴ 20 • written 5.7 years ago by 87k
239
votes
176
replies
95k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 months ago by 43k • written 8.7 years ago by ★ 4.7k
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
21
votes
26
replies
9.6k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 6 weeks ago by ▴ 30 • written 4.4 years ago by 8.5k
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by • 0 • written 10.2 years ago by 100k
65
votes
15
replies
14k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 11 months ago by 43k • written 5.6 years ago by 16k
3
votes
4
replies
3.6k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 11 months ago by 43k • written 5.5 years ago by ▴ 340
0
votes
0
replies
1.3k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 11 months ago by 43k • written 5.7 years ago by • 0
20
votes
2
replies
8.1k
views
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
2
votes
0
replies
1.4k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 11 months ago by 43k • written 5.9 years ago by ▴ 340
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 11 months ago by 43k • written 6.0 years ago by ▴ 340
3
votes
4
replies
4.5k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 11 months ago by 43k • written 6.0 years ago by ★ 2.5k
143 results • Page 2 of 3
Recent Votes
Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: Mapping ortholog human and mouse transcript
C: Kallisto missing Bootstrap
Answer: Very low RNA splicing rate for pulmonary AT2 cells
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
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Recent Replies
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller? by Medhat 9.7k
"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position. This co…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt by salias • 0
Fungal ITS2 region (length is really variable so read-through can be an issue)
Answer: Is it possible to bulk download files from GEO repository? by noodle ▴ 570
Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS acc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt by GenoMax 141k
Check a random sampling of reads to make sure the adapters are being removed. You may also want to blast a few reads to ensure that there i…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt by salias • 0
Many thanks for your comment. If read-through is happening, shouldn't Cutadapt being taking care of that there? I provided to the Cutadapt …
Comment: How should I make kallisto indexes? by bioinfo ▴ 150
Thank you. I will read the documentation you attached. Are you going to slowly phase out the not kb ref commands? Also, does the t2g.txt fi…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt by GenoMax 141k
> I need to understand why is this happening More than likely you have library fragments that are shorter than the length of sequencing. W…
Comment: Genbank File Format by Mensur Dlakic ★ 27k
I think this is a question for CLC support. It should be trivial for them to combine these fields into one. In other words, you need a bett…
Answer: Programmatically retrieving positions of protein active site residues by Mensur Dlakic ★ 27k
Although this probably doesn't qualify as `programmatically retrieving positions`, you can always do it by sequence alignments. This can be…
Answer: metagenomic virome quality assessment by Mensur Dlakic ★ 27k
The error message points to a problem with `prodigal-gv`. What happens when you type `prodigal-gv` on the command line? It is never a go…
Comment: Programmatically retrieving positions of protein active site residues by Wayne ★ 2.0k
"I have seen other similar posts but a lot of the tools and websites suggested are down." Please show & share your research as part of you…
Comment: Software to separate reads from different individuals by njornet ▴ 20
No... the extracted sample is already a mix so no way to barcode
Comment: Very low RNA splicing rate for pulmonary AT2 cells by e.r.zakiev ▴ 200
For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf` as I did, also observed an important…
Answer: Very low RNA splicing rate for pulmonary AT2 cells by e.r.zakiev ▴ 200
Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
Comment: Genbank File Format by GenoMax 141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
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