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66
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38
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21k
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22 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 3 days ago by • 0 • written 7.5 years ago by ★ 7.3k
69
votes
1
reply
44k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 7.8 years ago by 11k
5
votes
0
replies
175
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
16 days ago by rpolicastro 5.1k
224
votes
175
replies
68k
views
72 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 20 days ago by 32k • written 5.7 years ago by ★ 4.3k
9
votes
0
replies
269
views
Tutorial: Greatly speed up conda by using mamba
software
21 days ago by rpolicastro 5.1k
6
votes
0
replies
131
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
16 days ago by rpolicastro 5.1k
7
votes
2
replies
178
views
Tutorial: Installing an updated R version (>=4.0) using conda
R software error Tutorial
updated 25 days ago by 12k • written 25 days ago by ▴ 480
7
votes
1
reply
144
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
27 days ago by Kevin Blighe 72k
10
votes
6
replies
881
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 27 days ago by ▴ 730 • written 7 months ago by 5.1k
12
votes
2
replies
224
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
16 days ago by rpolicastro 5.1k
143
votes
34
replies
49k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 29 days ago by ▴ 120 • written 8.4 years ago by ★ 1.6k
4
votes
2
replies
918
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R linux bioinformatics Tutorial
updated 4 weeks ago by • 0 • written 9 weeks ago by ▴ 40
10
votes
2
replies
767
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
5 weeks ago by Hamid Ghaedi ★ 1.3k
4
votes
0
replies
552
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
11 days ago by ATpoint 48k
13
votes
0
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part1
methylation cancer R Tutorial
6 weeks ago by Hamid Ghaedi ★ 1.3k
67
votes
32
replies
9.6k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 6 weeks ago by • 0 • written 2.8 years ago by ★ 1.1k
29
votes
11
replies
3.7k
views
7 follow
Tutorial: Generating consensus sequence from bam file
bam fasta consensus Tutorial
updated 7 weeks ago by • 0 • written 2.1 years ago by 14k
10
votes
7
replies
5.4k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 8 weeks ago by 6.9k • written 22 months ago by ▴ 260
228
votes
32
replies
67k
views
22 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 8 weeks ago by ▴ 10 • written 7.5 years ago by 19k
39
votes
8
replies
2.5k
views
7 follow
Tutorial: Gene Set Enrichment Analysis
microarray RNA-Seq Tutorial enrichment GSEA
5 days ago by Hamid Ghaedi ★ 1.3k
3
votes
0
replies
437
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap Tutorial
11 weeks ago by GenoMax 99k
6
votes
0
replies
1.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
11 weeks ago by GenoMax 99k
5
votes
0
replies
624
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
11 weeks ago by GenoMax 99k
7
votes
1
reply
435
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 3 months ago by 48k • written 3 months ago by ★ 10k
34
votes
9
replies
8.9k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
tutorial flow cytometry Tutorial single cell
written 7.0 years ago by ★ 1.9k
2
votes
0
replies
640
views
Tutorial: Best Python Course
python Tutorial ad
updated 3 months ago by 15k • written 3 months ago by ▴ 20
10
votes
3
replies
3.6k
views
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 3 months ago by ▴ 220 • written 8 months ago by ▴ 70
0
votes
1
reply
1.6k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 4 months ago by • 0 • written 2.7 years ago by ▴ 200
70
votes
13
replies
11k
views
12 follow
Tutorial: Exploring cancer mutation data portals
Cancer Data Portal Mutation TCGA ICGC Tutorial
4 months ago by Malachi Griffith 18k
4
votes
10
replies
2.9k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation Tutorial DMR
4 months ago by dec986 ▴ 260
41
votes
6
replies
9.6k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
4 months ago by Cyriac Kandoth 5.5k
5
votes
2
replies
2.7k
views
Tutorial: bam2rpkm by bedtools
RNA-Seq bam rpkm bedtools Tutorial
updated 4 months ago by 48k • written 3.5 years ago by ▴ 110
16
votes
11
replies
4.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
4 months ago by Ram 32k
40
votes
33
replies
4.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
4 months ago by Ram 32k
80
votes
6
replies
13k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 5 months ago by ▴ 30 • written 2.6 years ago by 14k
15
votes
40
replies
12k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 5 months ago by ★ 1.8k • written 4.8 years ago by ▴ 140
17
votes
3
replies
3.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
10 days ago by ATpoint 48k
7
votes
4
replies
2.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
RNA-Seq Transcriptomics Tutorial R bioconductor
6 months ago by Thind amarinder ▴ 130
24
votes
0
replies
1.4k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
6 months ago by Malachi Griffith 18k
10
votes
1
reply
1.3k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
COVID-19 fastv Tutorial SARS-CoV-2
6 months ago by chen ★ 2.1k
54
votes
47
replies
32k
views
20 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 6 months ago by • 0 • written 4.5 years ago by ★ 2.9k
9
votes
5
replies
956
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
STAR STARsolo 10x Chromium Tutorial
6 months ago by Kevin Blighe 72k
13
votes
16
replies
2.6k
views
7 follow
Tutorial: Create de novo repeat library
annotation repeat de-novo Tutorial
6 months ago by Juke34 ★ 5.3k
0
votes
0
replies
270
views
Tutorial: BrainArray CDF, annotation, etc
brainarray cdf db Tutorial
7 months ago by Kevin Blighe 72k
30
votes
0
replies
2.4k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
RNA-Seq batch correction edgeR ma-plot Tutorial
7 months ago by ATpoint 48k
8
votes
0
replies
575
views
Tutorial: Long versus wide data for plotting genomics data in R.
R tidyverse ggplot2 Tutorial data.table
16 days ago by rpolicastro 5.1k
67
votes
68
replies
10k
views
16 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 15 days ago by ▴ 910 • written 3.2 years ago by 72k
104
votes
66
replies
24k
views
20 follow
Tutorial: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
ENA Fastq fastq-dump aspera Tutorial
updated 8 months ago by ▴ 30 • written 2.8 years ago by 48k
83
votes
15
replies
22k
views
16 follow
Tutorial: Heatmaps in R
heatmap R Tutorial
8 months ago by Jean-Karim Heriche 24k
1
vote
1
reply
397
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed txt bed2txt sequencing Tutorial
8 months ago by opheevallee • 0
328 results • Page 1 of 7
Recent Votes
Parallel haplotyping
Comment: Meaning letters in TCGA sample barcode field
Comment: Meaning letters in TCGA sample barcode field
Answer: MASURCA error for multiple entries
Comment: Finding how many times a nucleotide appear in the same position
Normalization of ATAC SEQ data for the proper deeptools heatmap
Methylation frequency + and - strand
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Recent Replies
Comment: Download all Bacteria accession list from NCBI by GenoMax 99k
If you have access to `nr` blast database then use `blastdbcmd` which is part of `blast+` package. blastdbcmd -db nr -taxids 2 -outfmt…
Comment: Download all Bacteria accession list from NCBI by GenoMax 99k
A lot of records are going to be `WP*` accessions which point to multiple organisms. Something to keep in mind.
Comment: Download all Bacteria accession list from NCBI by Kevin Blighe 72k
A related Python script that you could use (search by FASTA title): https://www.biostars.org/p/279584/#279811
Comment: short length amino acids by GenoMax 99k
> Can anybody help me how to blast them locally ? You can install `blast` program locally and use that. BLAST Handbook from NCBI: https://…
Comment: Meaning letters in TCGA sample barcode field by Kevin Blighe 72k
You are welcome, Sumit.
Comment: Precision of variant calling (INDELs) by desouzareis.r ▴ 220
Hi, yes it could. You can compare coverage between them, especially in regions where there are false positive and false negative variants r…
Comment: hello ever one by ATpoint 48k
If you enjoy chatting please feel free to join our Slack channel: https://www.biostars.org/p/305186/
Comment: hello ever one by GenoMax 99k
Biostars does not have an `Introductions` tradition. I don't want to delete this post because it may ban your account. Please do not post t…
Comment: Meaning letters in TCGA sample barcode field by sumitguptabt • 0
Thank you so much @kevin I will look into it and update you ASAP. BW Sumit
Comment: MASURCA error for multiple entries by Kevin Blighe 72k
Great to hear - thank you.
Comment: Meaning letters in TCGA sample barcode field by Kevin Blighe 72k
Hi, you can search for these here: https://portal.gdc.cancer.gov/ They seem to be from Clinical Proteomic Tumor Analysis Consortium (CPTAC)
Comment: GATK 4 and Spark multithreading by Victoria • 0
I am sorry, I didn't realise that wasn't allowed, I have deleted the other post.
Comment: Meaning letters in TCGA sample barcode field by sumitguptabt • 0
@krushnach80 Thank you, dear, These samples are from: cancer types: bronchus and lung, subtype: adenomas and adenocarcinomas. The data is H…
Comment: Meaning letters in TCGA sample barcode field by krushnach80 ▴ 910
what samples are these which tissue type?
Comment: Meaning letters in TCGA sample barcode field by sumitguptabt • 0
@kevin would you please help?
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