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345 results • Page
2 of 7
Sort: Rank
Rank
Views
Votes
Replies
234
votes
176
replies
79k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 4 weeks ago by
Ram
36k • written 7.0 years ago by
TriS
★ 4.6k
6
votes
0
replies
1.1k
views
Tutorial:
data.frames in R: How vectorization can save you time and heartache
R
16 months ago by
rpolicastro
9.4k
8
votes
1
reply
793
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk
fasta
Tutorial
17 months ago by
Kevin Blighe
82k
15
votes
9
replies
3.5k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R
tidyverse
gene
Tutorial
updated 11 months ago by
krushnach80
★ 1.1k • written 23 months ago by
rpolicastro
9.4k
12
votes
2
replies
859
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
Tutorial
16 months ago by
rpolicastro
9.4k
147
votes
35
replies
56k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
Tutorial
next-gen
updated 3 months ago by
Bramadi Arya
• 0 • written 9.7 years ago by
vijay
★ 1.6k
14
votes
2
replies
2.2k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
methylation
RNA-Seq
R
cancer
Tutorial
17 months ago by
Hamid Ghaedi
★ 2.6k
4
votes
0
replies
1.4k
views
Tutorial:
Building mosdepth on macOS
mosdepth
nim
Tutorial
16 months ago by
ATpoint
64k
7
votes
6
replies
3.0k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software
clusterProfiler
Tool
rna-seq
tool
updated 11 months ago by
cpad0112
21k • written 17 months ago by
Novogene
▴ 160
15
votes
7
replies
10.0k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
Seurat
clonotyping
VDJ
sc-RNAseq
Tutorial
updated 18 months ago by
Friederike
8.4k • written 3.2 years ago by
atakanekiz
▴ 300
270
votes
33
replies
84k
views
24 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 6 months ago by
tshtatland
▴ 100 • written 8.8 years ago by
Obi Griffith
20k
5
votes
0
replies
2.9k
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
18 months ago by
GenoMax
119k
10
votes
0
replies
3.3k
views
Tutorial:
Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
Tutorial
18 months ago by
GenoMax
119k
10
votes
0
replies
1.9k
views
Tutorial:
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
Tutorial
18 months ago by
GenoMax
119k
11
votes
1
reply
1.8k
views
Tutorial:
Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
Tutorial
updated 8 months ago by
ATpoint
64k • written 19 months ago by
Mensur Dlakic
★ 20k
40
votes
9
replies
10k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
Tutorial
flow-cytometry
9 months ago by
Ahill
★ 1.9k
0
votes
1
reply
2.1k
views
Tutorial:
Getting the lineage of an organism from NCBI taxonomy data
taxonomy
python
biosql
Tutorial
updated 20 months ago by
biofysikos
• 0 • written 4.0 years ago by
vimalkvn
▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 10 months ago by
Ram
36k • written 8.2 years ago by
Malachi Griffith
19k
6
votes
10
replies
3.9k
views
Tutorial:
Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation
Tutorial
DMR
20 months ago by
dec986
▴ 340
41
votes
6
replies
11k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf
vcf
ensembl
tcga
somatic
Tutorial
20 months ago by
Cyriac Kandoth
5.8k
5
votes
2
replies
3.9k
views
Tutorial:
bam2rpkm by bedtools
RNA-Seq
bam
rpkm
bedtools
Tutorial
updated 20 months ago by
ATpoint
64k • written 4.8 years ago by
jmzeng1314
▴ 130
16
votes
11
replies
7.0k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
Tutorial
3 days ago by
Ram
36k
41
votes
33
replies
6.2k
views
8 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta
how-to
documentation
Tutorial
20 months ago by
Ram
36k
94
votes
6
replies
19k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
snakemake
conda
workflow
Tutorial
updated 21 months ago by
psschlogl
▴ 50 • written 3.9 years ago by
finswimmer
15k
17
votes
40
replies
15k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
run
easy
orthomcl
all-v-all
mcl
Tutorial
updated 21 months ago by
Buffo
★ 1.9k • written 6.1 years ago by
Esaie
▴ 160
23
votes
4
replies
5.4k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap
chip-seq
atac-seq
heatmap
Tutorial
updated 13 months ago by
MatthewP
★ 1.1k • written 3.0 years ago by
ATpoint
64k
13
votes
4
replies
3.8k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
R
RNA-Seq
Transcriptomics
Tutorial
bioconductor
6 months ago by
Thind amarinder
▴ 270
26
votes
0
replies
1.8k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
variant
interpretation
annotation
clinical
cancer
Tutorial
22 months ago by
Malachi Griffith
19k
10
votes
1
reply
1.8k
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
22 months ago by
chen
★ 2.4k
60
votes
49
replies
37k
views
22 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
R
plotly
volcano plot
Tutorial
updated 15 months ago by
Ram
36k • written 5.9 years ago by
steve
★ 3.2k
10
votes
7
replies
3.6k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
STAR
STARsolo
10x
Chromium
Tutorial
updated 7 months ago by
GenoMax
119k • written 23 months ago by
Kevin Blighe
82k
15
votes
17
replies
5.6k
views
9 follow
Tutorial:
Create de novo repeat library
Tutorial
repeat
annotation
de-novo
updated 12 months ago by
tshittu
• 0 • written 2.7 years ago by
Juke34
★ 7.2k
0
votes
0
replies
667
views
Tutorial:
BrainArray CDF, annotation, etc
brainarray
cdf
db
Tutorial
23 months ago by
Kevin Blighe
82k
37
votes
0
replies
4.8k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
RNA-Seq
batch correction
edgeR
ma-plot
Tutorial
23 months ago by
ATpoint
64k
10
votes
0
replies
1.7k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
R
tidyverse
ggplot2
Tutorial
data.table
16 months ago by
rpolicastro
9.4k
75
votes
70
replies
14k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
Tutorial
david
updated 6 months ago by
Kristy
• 0 • written 4.5 years ago by
Kevin Blighe
82k
1
vote
1
reply
877
views
Tutorial:
Downloading GnuWin and using to convert txt to bed file for windows users
bed
txt
bed2txt
sequencing
Tutorial
2.0 years ago by
opheevallee
• 0
4
votes
3
replies
3.6k
views
Tutorial:
How to get full taxonomy classification using taxize and myTAI
taxonomy
tool
R
Tutorial
updated 14 months ago by
DNAngel
▴ 210 • written 4.4 years ago by
Daniel
★ 3.9k
4
votes
1
reply
843
views
Tutorial:
Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED
BEDtools
Tutorial
Video
Lesson
2.0 years ago by
sdsubaru33
▴ 40
72
votes
59
replies
21k
views
15 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes
PCA
VCF
PLINK
Tutorial
updated 10 months ago by
sara27888
• 0 • written 4.9 years ago by
Kevin Blighe
82k
3
votes
0
replies
2.1k
views
Tutorial:
Sorting GFF/GTF files
annotation
gff
gtf
sort
Forum
Tutorial
2.1 years ago by
Juke34
★ 7.2k
20
votes
6
replies
4.4k
views
Tutorial:
Open Targets and programmatic access
drug
API
bioinformatics
open targets
disease
Tutorial
2.1 years ago by
Denise CS
★ 5.2k
2
votes
2
replies
1.2k
views
Tutorial:
Human mitochondrial DNA annotation in SnpEff
SNP
snpEff
Annotation
Tutorial
chrMT
2.1 years ago by
Arup Ghosh
3.0k
10
votes
3
replies
1.3k
views
Tutorial:
FASTA file split
Tutorial
split
fasta
tutorial
8 weeks ago by
Juke34
★ 7.2k
0
votes
0
replies
872
views
Tutorial:
VIDEO: Installing BLAST Databases on Your Own Computer
sequence
BLAST databases
Linux
MacOSX
Tutorial
2.2 years ago by
brian.fristensky
▴ 280
0
votes
0
replies
652
views
Tutorial:
VIDEO: BLAST Searches Through a Data Science Lens
sequence
BLAST
Data Science
Covid19
Tutorial
2.2 years ago by
brian.fristensky
▴ 280
2
votes
1
reply
1.0k
views
Tutorial:
A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2
COVID-19
viruses
fastv
Tutorial
2.2 years ago by
chen
★ 2.4k
65
votes
25
replies
22k
views
14 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq
tutorial
Tutorial
updated 2.3 years ago by
Ram
36k • written 8.5 years ago by
Istvan Albert
94k
58
votes
41
replies
17k
views
16 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow
pbalign
pacbio
polishing
smrt limk
Tutorial
updated 2.3 years ago by
zjl1983
• 0 • written 4.9 years ago by
Rox
★ 1.4k
20
votes
7
replies
5.2k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
RNA-Seq
R
ggplot2
Tutorial
2.3 years ago by
ahmad mousavi
▴ 710
345 results • Page
2 of 7
Recent Votes
Why the result of GSEA and ssGSEA is different?
4-group RNAseq experiment- GSEA vs ssGSEA?
Are upset plots bad for differential expression analysis?
Answer: Are upset plots bad for differential expression analysis?
Answer: extracting sequences from a bam file
A: Best Genome Assembler and Genome Annotation tools and pipelines
Top/best RNAseq workflow including anlaysis results for function annotation
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Recent Replies
Answer: phylip format sequence name/header issue
by
Mensur Dlakic
★ 20k
Phylip format can have an arbitrary number of characters in header, but not all the programs will tolerate it. MrBayes, for example, has no…
Answer: phylip format sequence name/header issue
by
Michael Dondrup
52k
I assume you have the sequences in a FASTA file. I recommend to shorten the sequences in FASTA format already, then convert to phylip forma…
Comment: Extract sequences from a list of ID
by
Neel
▴ 20
Thank you....It has been done.
Comment: SNV, CNA, SV
by
Vincent Laufer
★ 2.2k
what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
Comment: Why weblogo of biopython doesn't work?
by
Plus
• 0
Yes. I can try the web version of WebLogo, but I just want to know what kind of problem can induce to make a corrupted file by using Motif.…
Comment: Difference between clusterProfiler and gProfileR
by
Arup Ghosh
3.0k
> The GO terms output by gprofileR are generally quite similar to those > output by clusterProfiler, but there are small differences due to…
Comment: hgmd variants from Ensembl
by
Sanjar
▴ 140
Did you figure out how to do this?
Comment: Why weblogo of biopython doesn't work?
by
Arup Ghosh
3.0k
The `weblogo` module uses the web version of weblogo service and it seems the module is not working as intended. Instead of returning an im…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
appropiate
▴ 40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID
by
GenoMax
119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes?
by
manaswwm
▴ 260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
cmdcolin
★ 2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit
by
ATpoint
64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
Answer: download just a chromosome from SRA toolkit
by
shelkmike
▴ 660
No, its impossible. Sequencing reads in SRA are not partitioned by chromosomes.
Comment: Extract sequences from a list of ID
by
Neel
▴ 20
Hi, i want to extract seq from list of id but Seqkit gives this below error and empty output file generated [WARN] symbol ">" detected…
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