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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
Biostar
10 • written 4.4 years ago by
Istvan Albert
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
Rob
▴ 40 • written 11 months ago by
Kevin Blighe
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
vel
• 0 • written 7.5 years ago by
Irsan
★ 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
Eric Normandeau
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
Ram
32k • written 5.7 years ago by
TriS
★ 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
dariober
12k • written 29 days ago by
Nitin Narwade
▴ 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
svlachavas
▴ 730 • written 7 months ago by
rpolicastro
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
ATpoint
48k • written 4 weeks ago by
GoldenRetriever
▴ 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
juanjo75es
▴ 120 • written 8.4 years ago by
vijay
★ 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
jessicapnoya
• 0 • written 10 weeks ago by
giessen_garten
▴ 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
volkanergin
• 0 • written 2.8 years ago by
egeulgen
★ 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
zjamal.msbi19rcms
• 0 • written 2.1 years ago by
finswimmer
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
ATpoint
48k • written 8 weeks ago by
dare_devil
★ 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
Friederike
6.9k • written 22 months ago by
atakanekiz
▴ 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
ashotmarg2004
▴ 10 • written 7.5 years ago by
Obi Griffith
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
brian.fristensky
▴ 160 • written 12 weeks ago by
florian.grosmaire
• 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
ATpoint
48k • written 3 months ago by
GoldenRetriever
▴ 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
Kevin Blighe
72k • written 3 months ago by
dsh.shadi
• 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
ATpoint
48k • written 3 months ago by
stephanie
• 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
ATpoint
48k • written 3 months ago by
Mensur Dlakic
★ 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
Ahill
★ 1.9k
2
votes
0
replies
646
views
Tutorial:
Best Python Course
python
Tutorial
ad
updated 3 months ago by
cpad0112
15k • written 3 months ago by
ssai31935
▴ 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
darklings
▴ 220 • written 8 months ago by
lavinia.gordon
▴ 70
0
votes
3
replies
400
views
RNA-Seq analysis with Python
RNA-Seq
tutorial
python
data analysis
updated 4 months ago by
rpolicastro
5.1k • written 4 months ago by
edus_bioinfo
• 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
biofysikos
• 0 • written 2.7 years ago by
Vimal Kumar Velayudhan
▴ 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
ATpoint
48k • written 3.5 years ago by
jmzeng1314
▴ 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
cpad0112
15k • written 5 months ago by
harry
▴ 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
psschlogl
▴ 30 • written 2.6 years ago by
finswimmer
14k
0
votes
4
replies
202
views
Single cell RNASeq data with only R2.fastq
RNA-Seq
Tutorial
updated 5 months ago by
ATpoint
48k • written 5 months ago by
shenwei1376
• 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
Buffo
★ 1.8k • written 4.8 years ago by
Esaie
▴ 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 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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