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143 results • Page 2 of 3
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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
18
votes
2
replies
5.9k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 11 months ago by 43k • written 7.0 years ago by 5.3k
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
3
votes
2
replies
8.8k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.5k
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 11 months ago by 43k • written 7.1 years ago by ▴ 30
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
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
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
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
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
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
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
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
6
votes
1
reply
438
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
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
3
votes
1
reply
644
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
1
vote
1
reply
334
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
0
votes
1
reply
543
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
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 6.5 years ago by ★ 3.0k
7
votes
1
reply
2.3k
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
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
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
0
votes
1
reply
290
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
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
0
votes
1
reply
530
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
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
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
2
votes
1
reply
410
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
0
replies
217
views
Tutorial: Parsing HMMER output
HMMER
updated 5 weeks ago by 141k • written 5 weeks ago by ▴ 140
1
vote
0
replies
326
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
274
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
273
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
0
votes
0
replies
257
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
209
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
9 weeks ago by Novogene ▴ 420
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
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
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
0
votes
0
replies
1.6k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
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
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
677
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
0
votes
0
replies
371
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 850
4
votes
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
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
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
2
votes
0
replies
6.9k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 11 months ago by 43k • written 6.4 years ago by ▴ 320
3
votes
0
replies
225
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
9 weeks ago by Novogene ▴ 420
1
vote
0
replies
250
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
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
2
votes
0
replies
408
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
143 results • Page 2 of 3
Recent Votes
Answer: High Malat-1 expression in single cell data
Answer: High Malat-1 expression in single cell data
The Biostar Herald for Monday, April 29, 2024
A: Bam And Indexed Bam Files
High Malat-1 expression in single cell data
Segmentation fault using gemma
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Recent Replies
Comment: High Malat-1 expression in single cell data by dsull ★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
Comment: CWl and toil singularity image e.g busybox? Thank you by Fadi • 0
Where can I ask this question? Apparently this the place where you can help for toil?
Comment: Limma Analysis Agilent Microarray Data (GPL1708) by hagl ▴ 10
Dear Gordon, excuse me for not being specific regarding your advice. What would be the best way if I wanted to add new annotations to the …
Comment: Programmatically retrieving positions of protein active site residues by GenoMax 141k
While you wait to get answers, consider asking ChatGPT for a solution. You may be pleasantly surprised with pointers/code you will get.
Comment: High Malat-1 expression in single cell data by Kazo ▴ 10
When I perform differential analysis, the genes that could be considered as markers in this malat1 high cluster tend to be nuclear genes. D…
Comment: How to update R on ubuntu by GenoMax 141k
You can check where the application was installed using: https://unix.stackexchange.com/questions/39590/apt-get-install-where-does-it-go T…
Comment: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
"using RNA-seq for allele imbalanced gene expression" -> Not sure what you mean by that; thousands of studies (including some ongoing studi…
Comment: High Malat-1 expression in single cell data by Kazo ▴ 10
I have noticed in articles that people define low-quality clusters and remove them from the data, but they don't exactly explain what makes…
Answer: High Malat-1 expression in single cell data by dsull ★ 5.9k
I'm assuming you read https://kb.10xgenomics.com/hc/en-us/articles/360004729092-Why-do-I-see-high-levels-of-Malat1-in-my-gene-expression-da…
Comment: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
I actually advised you not to remove duplicate probes, especially as you seem to be use probe annotation that is very old and possibly out …
Comment: Segmentation fault using gemma by dimpleadiwal050896 • 0
Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you
Comment: Can I merge Hi-C fastq files from different lanes? by GenoMax 141k
If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
Comment: What should I consider as FASTA for dataset? by GenoMax 141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository? by GenoMax 141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2 by GenoMax 141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
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