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98 results • Page 2 of 2
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2
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0
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740
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Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 11 months ago by 43k • written 11 months ago by ▴ 20
1
vote
0
replies
706
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
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0
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706
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
11 months ago by Coremine Medical ▴ 20
0
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0
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703
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
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702
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
9 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
702
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 11 months ago by 43k • written 11 months ago by ★ 3.9k
5
votes
5
replies
679
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 16 days ago by • 0 • written 25 days ago by ★ 3.9k
1
vote
5
replies
679
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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670
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
3
votes
1
reply
659
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.6k
1
vote
0
replies
654
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
2
votes
3
replies
653
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
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623
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
11 months ago by Ming Tommy Tang ★ 3.9k
7
votes
0
replies
618
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.2k
2
votes
0
replies
600
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 8 months ago by 43k • written 8 months ago by 161k
6
votes
0
replies
588
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by 11k • written 3 months ago by ★ 3.9k
0
votes
1
reply
587
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
3
votes
2
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583
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by 82k • written 4 months ago by ▴ 120
0
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1
reply
568
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
1
vote
0
replies
560
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
6 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
560
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
9 months ago by Ming Tommy Tang ★ 3.9k
0
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0
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499
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 870
2
votes
0
replies
491
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
6
votes
1
reply
490
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
2
votes
1
reply
481
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 43k • written 4 months ago by ▴ 120
2
votes
0
replies
445
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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418
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 43k • written 5 months ago by ★ 3.9k
0
votes
0
replies
397
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 870
1
vote
1
reply
382
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
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378
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
376
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
363
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
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356
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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349
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
1
reply
318
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
314
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
313
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
replies
311
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
307
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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298
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
292
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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278
views
Tutorial: How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat single-cell ggplot2
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
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270
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
263
views
Tutorial: Parsing HMMER output
HMMER
updated 8 weeks ago by 142k • written 8 weeks ago by ▴ 140
3
votes
0
replies
256
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
12 weeks ago by Novogene ▴ 420
2
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0
replies
237
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
12 weeks ago by Novogene ▴ 420
1
vote
0
replies
226
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
4 weeks ago by Novogene ▴ 420
7
votes
1
reply
213
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 13 days ago by 14k • written 13 days ago by ▴ 360
98 results • Page 2 of 2
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The Biostar Herald for Monday, May 20, 2024
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A: ClusterProfiler : What is GeneRatio and BgRatio?
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C: Cleaning RNA-Seq data from rRNA
Answer: How to find identical sequences in genome fasta file (by Python or any possible
Merging/Concatenating Vcf Files
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Recent Replies
Answer: Generating Group/Cluster Lists from fastq files by GenoMax 142k
> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
Comment: Super ehancers by jared.andrews07 ★ 16k
Based on the [source code](https://bitbucket.org/young_computation/rose/src/feb35cb1d9556a76f8ac1f51521539bb30651343/ROSE_utils.py?at=maste…
Comment: HGVS Nomenclature of Multiple Indels found in Cis by Ram 43k
They're not addressing the actual question, just saying something tangentially related. It looks like their understanding of both consensus…
Comment: Super ehancers by Oburah • 0
Hello, i encountered this problem when running ROSE, Do anyone know how to solve it? python2.7 ROSE_main.py -g HG38 -i /home/hesborn/…
Answer: How to generate an Upset plot in R to plot the shared variants between cell free by zx8754 11k
Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array by fu_entomology ▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible by GenoMax 142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway by marco.barr ▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps by Bioinformatics_begginner ▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by GenoMax 142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps by Pierre Lindenbaum 161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps by DGTool ▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range by Matthias Zepper 4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range by marco.barr ▴ 130
If you write me the code you used I can help you more
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