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328 results • Page
2 of 7
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1
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1
reply
402
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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
1
vote
2
replies
2.2k
views
Tutorial:
How to get full taxonomy classification using taxize and myTAI
taxonomy
tool
R
Tutorial
updated 8 months ago by
wangdepin5135
• 0 • written 3.0 years ago by
Daniel
★ 3.8k
3
votes
1
reply
380
views
Tutorial:
Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED
BEDtools
Tutorial
Video
Lesson
8 months ago by
sdsubaru33
▴ 30
65
votes
61
replies
15k
views
14 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000 genomes
PLINK
PCA
Tutorial
8 months ago by
Kevin Blighe
72k
70
votes
56
replies
16k
views
13 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes
PCA
VCF
PLINK
Tutorial
8 months ago by
Kevin Blighe
72k
13
votes
0
replies
3.6k
views
Tutorial:
Using R in Conda
R
Tutorial
9 months ago by
rohitsatyam102
▴ 300
2
votes
0
replies
609
views
Tutorial:
Sorting GFF/GTF files
annotation
gff
gtf
sort
Forum
Tutorial
9 months ago by
Juke34
★ 5.3k
20
votes
6
replies
3.6k
views
Tutorial:
Open Targets and programmatic access
drug
API
bioinformatics
open targets
disease
Tutorial
9 months ago by
Denise CS
★ 5.1k
2
votes
2
replies
426
views
Tutorial:
Human mitochondrial DNA annotation in SnpEff
SNP
snpEff
Annotation
Tutorial
chrMT
9 months ago by
Arup Ghosh
2.8k
110
votes
115
replies
14k
views
18 follow
Tutorial:
Survival analysis with gene expression
survival analysis
cox
geo
gene expression
Tutorial
updated 10 months ago by
Hamtaro
▴ 10 • written 2.5 years ago by
Kevin Blighe
72k
10
votes
3
replies
593
views
Tutorial:
FASTA file split
fasta
split
tutorial
Tutorial
updated 10 months ago by
cpad0112
15k • written 10 months ago by
Juke34
★ 5.3k
0
votes
0
replies
443
views
Tutorial:
VIDEO: Installing BLAST Databases on Your Own Computer
sequence
BLAST databases
Linux
MacOSX
Tutorial
10 months ago by
brian.fristensky
▴ 160
0
votes
0
replies
317
views
Tutorial:
VIDEO: BLAST Searches Through a Data Science Lens
sequence
BLAST
Data Science
Covid19
Tutorial
10 months ago by
brian.fristensky
▴ 160
2
votes
1
reply
513
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
10 months ago by
chen
★ 2.1k
62
votes
25
replies
19k
views
12 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq
tutorial
Tutorial
updated 11 months ago by
Ram
32k • written 7.2 years ago by
Istvan Albert
87k
51
votes
41
replies
14k
views
16 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow
pbalign
pacbio
polishing
smrt limk
Tutorial
updated 11 months ago by
zjl1983
• 0 • written 3.6 years ago by
Rox
★ 1.3k
180
votes
46
replies
62k
views
30 follow
Tutorial:
Analysing Microarray Data In Bioconductor
tutorial
bioconductor
microarray
analysis
tutorial
Tutorial
updated 11 months ago by
lsbw
• 0 • written 8.6 years ago by
Obi Griffith
19k
19
votes
7
replies
3.9k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
RNA-Seq
R
ggplot2
Tutorial
12 months ago by
ahmad mousavi
▴ 520
4
votes
0
replies
652
views
Tutorial:
NIH CDE browser for TCGA clinical data CDE codes
tcga
nih
cde
metadata
Tutorial
12 months ago by
Kevin Blighe
72k
10
votes
17
replies
1.6k
views
Tutorial:
gene set filter/selection for training ab initio annotation tools
genome
gene
Tutorial
12 months ago by
Juke34
★ 5.3k
11
votes
1
reply
1.8k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
RNA-Seq
scRNA-seq
CITE-seq-count
Tutorial
12 months ago by
colindaven
★ 2.7k
9
votes
4
replies
3.2k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long reads
minion
oxford nanopore
Tutorial
13 months ago by
colindaven
★ 2.7k
0
votes
0
replies
420
views
Tutorial:
Training GeneMark-EP+ ab-initio tool
annotation
genemark
training
abinitio
Tutorial
13 months ago by
Juke34
★ 5.3k
2
votes
1
reply
1.2k
views
Tutorial:
How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
VCF Format
SNP Filtering
bcftools codes
Tutorial
13 months ago by
Asad Prodhan
▴ 10
5
votes
0
replies
1.2k
views
Tutorial:
How to run CWL with Nextflow
nextflow
cwl
Tutorial
14 months ago by
steve
★ 2.9k
129
votes
66
replies
30k
views
15 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
14 months ago by
Kevin Blighe
72k
5
votes
2
replies
1.2k
views
Tutorial:
Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
bedtools closest
closestBed
preRNA
bedtools
Tutorial
15 months ago by
linuxborg2
▴ 10
46
votes
3
replies
2.8k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
tutorial
Tutorial
how-to
15 months ago by
ATpoint
48k
19
votes
9
replies
5.3k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
tutorial
Tutorial
updated 15 months ago by
zubenel
▴ 110 • written 7.8 years ago by
Medhat
8.9k
250
votes
39
replies
124k
views
27 follow
Tutorial:
How to download raw sequence data from GEO/SRA
GEO
SRA
fastq
bam
download
Tutorial
updated 2 days ago by
cicindel
▴ 70 • written 6.6 years ago by
Obi Griffith
19k
58
votes
26
replies
7.7k
views
7 follow
Tutorial:
Parallel processing in R
R
Tutorial
biocparallel
mclapply
foreach
17 months ago by
Kevin Blighe
72k
19
votes
15
replies
2.3k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
Tutorial
17 months ago by
Shicheng Guo
★ 8.6k
18
votes
4
replies
1.5k
views
Tutorial:
Bash One-liners collection on Github
bash-oneliners
linux
shell
bioinformatics
bash
Tutorial
written 23 months ago by
nim.1111.ou
▴ 160
42
votes
1
reply
31k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
tutorial
Tutorial
updated 18 months ago by
ATpoint
48k • written 9.0 years ago by
MSU course 2011
▴ 510
14
votes
7
replies
4.1k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
R
HOMER
peaks
Tutorial
20 months ago by
steve
★ 2.9k
2
votes
0
replies
2.0k
views
Tutorial:
Calculation of TSS Scores for ATAC-seq Data
next-gen
sequencing
Tutorial
21 months ago by
Sael
▴ 20
4
votes
1
reply
805
views
Tutorial:
Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0
Tutorial
updated 22 months ago by
Leon
▴ 120 • written 22 months ago by
Shicheng Guo
★ 8.6k
11
votes
18
replies
5.7k
views
8 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat
single cell
RNA-Seq
TCR
Tutorial
updated 22 months ago by
atakanekiz
▴ 260 • written 22 months ago by
jared.andrews07
9.3k
0
votes
0
replies
444
views
Tutorial:
Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
Tutorial
22 months ago by
Shicheng Guo
★ 8.6k
16
votes
11
replies
11k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
cBioportal
TCGA
data_retrieval
RNASeq
R
Tutorial
updated 22 months ago by
raffael.azevedo
▴ 30 • written 4.5 years ago by
TriS
★ 4.3k
10
votes
5
replies
12k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
Tutorial
updated 2.1 years ago by
moxu
▴ 480 • written 2.7 years ago by
Shicheng Guo
★ 8.6k
33
votes
15
replies
14k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
R
TCGA
GDC
next-gen
Tutorial
updated 2.1 years ago by
david.peeney
▴ 30 • written 4.5 years ago by
martinguerrerog89
▴ 300
6
votes
3
replies
3.2k
views
Tutorial:
Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
sequencing
alignment
rna-seq
gene
Tutorial
updated 2.1 years ago by
al-ash
▴ 150 • written 2.5 years ago by
contact
▴ 40
2
votes
11
replies
2.5k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
merge
bcftools
Tutorial
2.2 years ago by
jaybee
▴ 80
0
votes
0
replies
592
views
Tutorial:
Introduction to Gen3 Webinar
datacommons
bigdata
opensource
gen3
Tutorial
2.2 years ago by
Danielle
▴ 310
4
votes
2
replies
2.8k
views
Tutorial:
Introduce OpenGene: an open source library for processing NGS data
sequencing
OpenGene
Julia
NGS
Tutorial
updated 2.2 years ago by
sudharshanva
• 0 • written 5.2 years ago by
chen
★ 2.1k
28
votes
4
replies
2.7k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
Tutorial
2.2 years ago by
Jean-Karim Heriche
24k
59
votes
6
replies
8.1k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
tools
bioinformatics
Tutorial
2.3 years ago by
Medhat
8.9k
5
votes
2
replies
1.4k
views
Tutorial:
NCBI submissions: SRA and TSA
NCBI
TSA
SRA
RNA-Seq
tutorial
Tutorial
2.4 years ago by
saraoppenheim
▴ 50
5
votes
0
replies
923
views
Tutorial:
NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
structural variation
dbvar
Tutorial
updated 2.4 years ago by
ATpoint
48k • written 2.4 years ago by
lonphan
▴ 50
328 results • Page
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Recent Votes
Answer: How to combine 2 incomplete GTF
Answer: How to combine 2 incomplete GTF
A: Correct Way To Parse A Fasta File In Python
How to combine 2 incomplete GTF
How to combine 2 incomplete GTF
How to combine 2 incomplete GTF
How to combine 2 incomplete GTF
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9.3k
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Juke34
★ 5.3k
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Recent Replies
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
rigth, it is a ChIP seq analysis
Comment: how to select peaks at not transcribed genes
by
ATpoint
48k
Which type data are we talking about? What was the experiment? There are literally no details in this question right now. It the assay meas…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Thank yo so much Juke!
Comment: MASURCA output
by
kilcdincer
▴ 10
Thank you. I understood ploidy part. My genome is supposed to belong to diploid Candida albicans. And genome size of diploid Candida alb…
Answer: How to combine 2 incomplete GTF
by
Juke34
★ 5.3k
To give more precision to the @genomax comment: `agat_sp_compare_annotations.pl` will tell you the differences. Then you can choose to …
Comment: GSEA for RNA_seq dataset
by
ATpoint
48k
No problem. I am not really familiar with what the GSEA implementation from the Broad institute does. I personally use fgsea from Bioconduc…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Thank you!! I will try it :)
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
you mean in the call peaks? And what are those 232 not annotated peaks?aren't they tss associated to not transcribed genes?
Comment: How to combine 2 incomplete GTF
by
GenoMax
99k
Compare annotation tool `agat_sp_compare_annotations.pl` from [AGAT toolkit][1]. Install [**AGAT**][2] using `conda`. [1]: https://gith…
Comment: GSEA for RNA_seq dataset
by
1961012
• 0
I am really sorry for asking for clarification because I am a beginner. I already used all genes (normalized and filtered) for GSEA using …
Comment: Snakemake with bwa_mem2_mem unable to open the ref file and doesn' t work
by
aka
• 0
I work in a research laboratory that has specific demands that make the general pipeline not fit, I have to create it from scratch, but tha…
Comment: Extract chromosome 1 - 22 fasta file
by
shubhamkumbhar420
• 0
Thank you for your response! It worked !!!
Answer: How to combine 2 incomplete GTF
by
Michael Dondrup
48k
I made this perl script to compare two GFF files. It might be useful after some modifications (changing GFF version to 2?). Needs BioPerl i…
Comment: Snakemake with bwa_mem2_mem unable to open the ref file and doesn' t work
by
aka
• 0
Hi, Thank you for your help! For the 1st it's a mistake sorry I change it and it's still the same. For the 2nd yes I am sure because wit…
Answer: R command worked yesterday, but stalls today?
by
ATpoint
48k
Make it simple and download that RDS file from command line with something like `wget`, this will give a status bar. Once downloaded just r…
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