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128 results • Page 1 of 3
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7
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1
reply
179
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Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 7 days ago by 14k • written 7 days ago by ▴ 360
5
votes
5
replies
653
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 11 days ago by • 0 • written 19 days ago by ★ 3.9k
76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
19 days ago by Kevin Blighe 88k
5
votes
13
replies
1.9k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 24 days ago by 82k • written 25 days ago by ★ 1.7k
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 25 days ago by 6.4k • written 16 months ago by ▴ 130
1
vote
0
replies
215
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
26 days ago by Novogene ▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 26 days ago by • 0 • written 3.6 years ago by 3.2k
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 6 weeks ago by 100k • written 8.2 years ago by 43k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 weeks ago by 43k • written 6.2 years ago by 88k
0
votes
0
replies
250
views
Tutorial: Parsing HMMER output
HMMER
updated 7 weeks ago by 142k • written 7 weeks ago by ▴ 140
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 weeks ago by ▴ 30 • written 7.6 years ago by ▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 9 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
229
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
11 weeks ago by Novogene ▴ 420
3
votes
0
replies
248
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
11 weeks ago by Novogene ▴ 420
6
votes
0
replies
574
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
0
replies
342
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
3 months ago by Ming Tommy Tang ★ 3.9k
1
vote
5
replies
652
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
2
replies
574
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 4 months ago by ▴ 120
2
votes
1
reply
463
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
0
votes
1
reply
308
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
263
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
279
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
302
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
299
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
365
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
265
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
1
vote
0
replies
304
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
0
votes
0
replies
346
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
1
reply
571
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 4 months ago by ▴ 120
2
votes
0
replies
436
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
275
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
1
reply
367
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
3
replies
635
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
6
votes
1
reply
475
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
285
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 4 months ago by ▴ 120
39
votes
16
replies
37k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 months ago by 142k • written 3.7 years ago by ▴ 160
1
vote
0
replies
366
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
0
votes
0
replies
400
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 43k • written 5 months ago by ★ 3.9k
1
vote
0
replies
352
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
390
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 860
0
votes
0
replies
490
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 860
0
votes
4
replies
765
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
90
votes
48
replies
34k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 6 months ago by 43k • written 10.6 years ago by ★ 7.8k
1
vote
0
replies
546
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
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.3 years ago by ▴ 320
2
votes
0
replies
586
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
0
votes
1
reply
553
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
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
128 results • Page 1 of 3
Recent Votes
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
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Popular Question to Sofia • 0
Popular Question to jen ▴ 10
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Recent Replies
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Comment: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by GenoMax 142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file by ramiro.barrantes • 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
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