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Showing top results for tag: Tutorial • reset
584
votes
155
replies
64k
views
89 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 9 days ago by 10 • written 4.4 years ago by 87k
21
votes
4
replies
2.3k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
updated 3 days ago by ▴ 40 • written 11 months ago by 72k
66
votes
38
replies
21k
views
22 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 7 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
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 24 days ago by 32k • written 5.7 years ago by ★ 4.3k
7
votes
2
replies
196
views
Tutorial: Installing an updated R version (>=4.0) using conda
R software error Tutorial
updated 29 days ago by 12k • written 29 days ago by ▴ 480
7
votes
1
reply
151
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
4 weeks ago by Kevin Blighe 72k
10
votes
6
replies
887
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 4 weeks ago by ▴ 730 • written 7 months ago by 5.1k
12
votes
2
replies
235
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
20 days ago by rpolicastro 5.1k
5
votes
8
replies
181
views
A layman trying to understand what a FASTA file is
RNA-Seq sequencing next-gen gene tutorial
updated 4 weeks ago by 48k • written 4 weeks ago by ▴ 40
1
vote
5
replies
144
views
Read count using htseq-count.
RNA-Seq gene rna-seq Assembly Tutorial
4 weeks ago by Saeed • 0
143
votes
34
replies
50k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 4 weeks ago by ▴ 120 • written 8.4 years ago by ★ 1.6k
4
votes
2
replies
942
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R linux bioinformatics Tutorial
updated 5 weeks ago by • 0 • written 10 weeks ago by ▴ 40
0
votes
0
replies
310
views
Job: Exciting Bioinformatician/Statistician Opportunity at Gladstone Insitutes (San Francisco)
R RNA-Seq genome sequencing Tutorial Job
5 weeks ago by janine.doerner ▴ 20
10
votes
2
replies
783
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
558
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
15 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 7 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 8 weeks ago by • 0 • written 2.1 years ago by 14k
3
votes
3
replies
326
views
Are there any tutorials available for Nanostring data differential expression analysis using DEseq2 ?
tutorial nanostring deseq2 limma
updated 8 weeks ago by 48k • written 8 weeks ago by ★ 1.4k
10
votes
7
replies
5.5k
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 9 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
9 days ago by Hamid Ghaedi ★ 1.3k
0
votes
1
reply
157
views
How to calculate dN/dS for all ortholog group ?
Hyphy dN/dS slac fel Tutorial
9 weeks ago by sadstudent • 0
3
votes
0
replies
449
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
7
votes
0
replies
722
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
2
votes
6
replies
203
views
Blast + Alignement Shell Script
alignment script blast shell Tutorial
updated 12 weeks ago by ▴ 160 • written 12 weeks ago by • 0
12
votes
13
replies
304
views
K-mer sequencing vs sequence-alignment
next-gen alignment k-mer short-reads Tutorial
updated 3 months ago by 48k • written 3 months ago by ▴ 40
3
votes
3
replies
209
views
What is dbsnp file and how can I find it?
SNP snp Tutorial
updated 3 months ago by 72k • written 3 months ago by • 0
0
votes
1
reply
245
views
Running GSVA using open source RNA seq data
RNA-Seq R gene GSVA Tutorial
3 months ago by jacobelnaggar • 0
0
votes
0
replies
156
views
News: Tutorial on Detecting Structural Variants in ONT data
structural_variants ONT Tutorial News
updated 3 months ago by 48k • written 3 months ago by • 0
7
votes
1
reply
441
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
646
views
Tutorial: Best Python Course
python Tutorial ad
updated 3 months ago by 15k • written 3 months ago by ▴ 20
10
votes
3
replies
3.7k
views
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 4 months ago by ▴ 220 • written 8 months ago by ▴ 70
0
votes
3
replies
400
views
RNA-Seq analysis with Python
RNA-Seq tutorial python data analysis
updated 4 months ago by 5.1k • written 4 months ago by • 0
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
0
votes
0
replies
203
views
ribosomal protein transcript id download
transcript id human ribosomal protein Tutorial
updated 5 months ago by 15k • written 5 months ago by ▴ 20
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
0
votes
4
replies
202
views
Single cell RNASeq data with only R2.fastq
RNA-Seq Tutorial
updated 5 months ago by 48k • written 5 months ago by • 0
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
0
votes
0
replies
224
views
Package for RNA-Protein Interaction Network
RNA-Seq tutorial scRNA-seq single-cell
6 months ago by jvbeltran0122 ▴ 10
18
votes
5
replies
3.3k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
1 day ago by ATpoint 48k
50 results • Page 1 of 1
Recent Votes
Answer: Future of Microarrays
C: Calculate minor allele frequency from VCF
C: Get variant position knowing the gene name, base change, and NM#
TCGA patient variable data dictionary
Answer: TMM-Normalization
Iterating through paired-end reads in samtools / pysam
Answer: TMM-Normalization
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Recent Awards • All
Teacher to i.sudbery 11k
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Recent Replies
Comment: split vcf file into multiple files by Pierre Lindenbaum 135k
what is your shell ? what is the output of ${SHELL} ? are you using bash ? replace "bcftools view" with "echo" , what is the output ?
Comment: error in bowtie2 alignment by i.sudbery 11k
Dear pdhrati02 Given the age of this question and the slight difference in your question, I think you would be better off starting a new qu…
Comment: Create Mutational signature plot from vcf file. by nhaus ▴ 30
Unfortunately, it does not seem like this tool outputs this particular plot.
Comment: Convertion Of Gff3 To Gtf by daalsa98 ▴ 10
Oh, thanks!, I'll take a look and see if it works
Answer: Convertion Of Gff3 To Gtf by lieven.sterck 11k
you can have a look at the AGAT toolkit https://www.biostars.org/p/413510/ , there might be some tool in it that can do this.
Answer: Bam File: Change Chromosome Notation by Pierre Lindenbaum 135k
update 2021: I wrote http://lindenb.github.io/jvarkit/ConvertBamChromosomes.html
Answer: Future of Microarrays by GenoMax 99k
Arrays remain alive. Demise of arrays has been predicted for a few years but they continue to be used since they are a proven technology. D…
Answer: Create Mutational signature plot from vcf file. by amitpande74 ▴ 20
tried this ? [comutplotter][1] [1]: http://tardis.cgu.edu.tw/comutplotter/
Comment: DiffBind consensus peak extraction by wei.zhang • 0
Hi Rory, here is the information > sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu …
Comment: Can't count features with featurecount by Michael Dondrup 48k
That is a bit weird, so you cannot get around a QC. I suspect that your mRNA is degraded due to storage as FFPE and therefore only few read…
Comment: Skewed Betweenness Centrality values resulting in almost unusable PPI networks f by gemmalouisebaldock ▴ 20
Thank you for the response, may I just ask for clarification. 1) Are you saying that a solution could be to change my mapping from 0-0.7, …
Comment: [E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam' by jenyfer • 0
thanks but it still gives the same error `[E::idx_find_and_load] Could not retrieve index file for '/mnt/d/RNA-SEQ/SRR13532540/SRR13532540s…
Comment: Converting Braker2 gtf output to gff then genbank by Juke34 ★ 5.4k
Yes with an awk command throw out all lines with gene and transcript feature type (3rd column). Then reconstruct them by runing `agat_conve…
Answer: [E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam' by ATpoint 48k
Index it: `samtools index your.bam`
Comment: R and GEO by ATpoint 48k
First step is adding details. Which dataset?
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