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328 results • Page
1 of 7
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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
5
votes
0
replies
154
views
Tutorial:
Pipes in R: An introduction and some advanced tips and tricks.
R
12 days ago by
rpolicastro
5.1k
224
votes
175
replies
67k
views
72 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 16 days ago by
Ram
32k • written 5.7 years ago by
TriS
★ 4.3k
9
votes
0
replies
225
views
Tutorial:
Greatly speed up conda by using mamba
software
17 days ago by
rpolicastro
5.1k
6
votes
0
replies
122
views
Tutorial:
data.frames in R: How vectorization can save you time and heartache
R
12 days ago by
rpolicastro
5.1k
7
votes
2
replies
168
views
Tutorial:
Installing an updated R version (>=4.0) using conda
R
software error
Tutorial
updated 21 days ago by
dariober
12k • written 21 days ago by
Nitin Narwade
▴ 480
7
votes
1
reply
134
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk
fasta
Tutorial
23 days ago by
Kevin Blighe
72k
10
votes
6
replies
874
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R
tidyverse
gene
Tutorial
updated 23 days ago by
svlachavas
▴ 730 • written 7 months ago by
rpolicastro
5.1k
12
votes
2
replies
215
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
Tutorial
12 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 25 days ago by
juanjo75es
▴ 90 • written 8.4 years ago by
vijay
★ 1.6k
4
votes
2
replies
903
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R
linux
bioinformatics
Tutorial
updated 27 days ago by
jessicapnoya
• 0 • written 8 weeks ago by
giessen_garten
▴ 40
10
votes
2
replies
758
views
Tutorial:
Methylation Analysis Tutorial in R_part2
methylation
RNA-Seq
R
cancer
Tutorial
4 weeks ago by
Hamid Ghaedi
★ 1.3k
4
votes
0
replies
550
views
Tutorial:
Building mosdepth on macOS
mosdepth
nim
Tutorial
7 days ago by
ATpoint
47k
13
votes
0
replies
2.8k
views
Tutorial:
Methylation Analysis Tutorial in R_part1
methylation
cancer
R
Tutorial
5 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
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 6 weeks ago by
zjamal.msbi19rcms
• 0 • written 2.1 years ago by
finswimmer
14k
10
votes
7
replies
5.4k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
Seurat
clonotyping
VDJ
sc-RNAseq
Tutorial
updated 7 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 7 weeks ago by
ashotmarg2004
▴ 10 • written 7.5 years ago by
Obi Griffith
19k
39
votes
8
replies
2.4k
views
7 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
RNA-Seq
Tutorial
enrichment
GSEA
1 day ago by
Hamid Ghaedi
★ 1.3k
3
votes
0
replies
430
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
10 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
10 weeks ago by
GenoMax
99k
5
votes
0
replies
619
views
Tutorial:
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
Tutorial
10 weeks ago by
GenoMax
99k
7
votes
1
reply
423
views
Tutorial:
Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
Tutorial
updated 3 months ago by
ATpoint
47k • written 3 months ago by
Mensur Dlakic
★ 10k
34
votes
9
replies
8.8k
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
628
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
3.5k
views
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
Tutorial
updated 3 months ago by
darklings
▴ 220 • written 7 months ago by
lavinia.gordon
▴ 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
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
47k • written 3.5 years ago by
jmzeng1314
▴ 110
16
votes
11
replies
4.6k
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
psschlogl
▴ 30 • written 2.6 years ago by
finswimmer
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
Buffo
★ 1.8k • written 4.8 years ago by
Esaie
▴ 140
17
votes
3
replies
3.1k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap
chip-seq
atac-seq
heatmap
Tutorial
6 days ago by
ATpoint
47k
66
votes
39
replies
21k
views
20 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq
bioconductor
fpkm
Forum
Tutorial
updated 5 months ago by
Ram
32k • written 7.5 years ago by
Irsan
★ 7.3k
7
votes
4
replies
2.1k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
RNA-Seq
Transcriptomics
Tutorial
R
bioconductor
5 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
jg43486
• 0 • written 4.5 years ago by
steve
★ 2.9k
9
votes
5
replies
931
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
266
views
Tutorial:
BrainArray CDF, annotation, etc
brainarray
cdf
db
Tutorial
6 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
47k
8
votes
0
replies
567
views
Tutorial:
Long versus wide data for plotting genomics data in R.
R
tidyverse
ggplot2
Tutorial
data.table
12 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 10 days ago by
krushnach80
▴ 900 • written 3.1 years ago by
Kevin Blighe
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 7 months ago by
Brunox13
▴ 30 • written 2.8 years ago by
ATpoint
47k
83
votes
15
replies
22k
views
16 follow
Tutorial:
Heatmaps in R
heatmap
R
Tutorial
7 months ago by
Jean-Karim Heriche
24k
1
vote
1
reply
391
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
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Answer: Tool to find chromosome specific repeats
Answer: What Is The Total Size Of Hgdownload.Cse.Ucsc.Edu/Gbdb/Mm9
Comment: correct way of analyzing cell proportions in singlecell data
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Recent Replies
Answer: Expression of gene of interest across conditions in single-cell data
by
jared.andrews07
9.1k
Take a look at [dittoSeq](http://www.bioconductor.org/packages/release/bioc/vignettes/dittoSeq/inst/doc/dittoSeq.html) for viz options - it…
Comment: Extracting only tumor samples from Single cell RNASeq
by
jared.andrews07
9.1k
You need pre-defined variants for Vartrix. Typically it's used in conjuction with WGS/WES from bulk tissue to look for clonal variants in d…
Comment: Cell composition in each condition of single cell data
by
paria.alipour
▴ 20
Oh, I'm sorry. I already posted it in here the https://www.biostars.org/p/457243/#9464486. I've added the images
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This seems OK when one gene generates only one transcirpt. But when one gene has multiple transcripts, these code would return a table wher…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This seems feasible. But I want to convert tens of thousands of transcript IDs. Could you tell me how can I make it through sequene search?
Answer: bbmap, mapq and uniquelly mapped reads filtering
by
GenoMax
99k
Many threads exist that show how to extract uniquely mapped reads. Here are a couple of examples:<br> https://www.biostars.org/p/276216/#27…
Comment: Cell composition in each condition of single cell data
by
rpolicastro
5.1k
The images seem to be missing from your post
Comment: Limma experiment design and making contrasts
by
kra277
• 0
Thank you very much for this. Much appreciated.
Comment: Limma experiment design and making contrasts
by
Kevin Blighe
72k
Hi, these follow the same principles as formulae used in regression modelling, so, you may want to focus on that (when searching). What lim…
Comment: Limma experiment design and making contrasts
by
kra277
• 0
That is very insightful. Thank you very much for the answer. Also, if I may ask, could you please point me to the articles for understandin…
Comment: Keep values from VCF file into Ensembl VEP annotation
by
brunobsouzaa
▴ 510
Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
Comment: Raw read processing using trimmomatic
by
boczniak767
▴ 740
Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding…
Comment: should stop codon be counted as part of CDS
by
sullis02
• 0
Your github page appears to live here now https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md
Comment: How do I compare degree and betweenness centrality for different PPI networks?
by
Istvan Albert
87k
I am not all that knowledgeable of Cytoscapes features and scripting capabilities, but if it does not support that operation you can expo…
Comment: Creating reference genome for mapping and then selecting
by
Istvan Albert
87k
you would get the counts as you would get them in any other case, how do you know something maps to chromosome 1 of human genome? Because i…
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