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167 results • Page
1 of 4
Sort: Votes
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Views
Votes
Replies
202
votes
41
replies
23k
views
20 follow
Forum:
Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics
cram
gatk
galaxy
updated 4 hours ago by
Ram
38k • written 8.2 years ago by
William
★ 5.1k
39
votes
18
replies
26k
views
16 follow
extract only geneID and gene symbol from GTF file
gtf
python
genome
updated 2 hours ago by
Ram
38k • written 7.8 years ago by
catherine
▴ 220
38
votes
63
replies
17k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly
miseq
illumina
genome
updated 20 hours ago by
Ram
38k • written 10.0 years ago by
Leszek
4.2k
27
votes
13
replies
35k
views
10 follow
Survival Analysis Using Tcga Data
tcga
bioinformatician
updated 21 hours ago by
Ram
38k • written 8.9 years ago by
jack
▴ 500
23
votes
9
replies
120k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
juan.rosas1
▴ 70
18
votes
22
replies
6.7k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
Tutorial
annotation
updated 2 hours ago by
evoecogen
▴ 20 • written 3.2 years ago by
Juke34
7.5k
10
votes
12
replies
8.9k
views
6 follow
Extract several sequences from genome in FASTA format with genomic coordinates.
genome
blast
updated 2 hours ago by
Ram
38k • written 8.0 years ago by
Ander
▴ 50
10
votes
10
replies
2.6k
views
how I can install lumi, plier, simpleaffy, oligo classes, LMGene and siggens packages?
R
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
fi1d18
★ 4.1k
9
votes
3
replies
7.5k
views
removing outliers from RNA-seq data
outliers
WGCNA
RNA-Seq
R
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
jfertaj
▴ 110
9
votes
6
replies
2.6k
views
using cufflinks when investigating differential expression
RNA-Seq
differential-expression
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
sangita_b
▴ 80
9
votes
5
replies
5.1k
views
Forum:
Can I switch back to wet lab in phd after doing a master in bioinformatics?
wetlab
phd
bioinformatics
biology
Forum
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
blueearth205
▴ 10
8
votes
17
replies
2.8k
views
6 follow
Relative frequencies of the nucleotides in Fasta files
fasta
updated 1 hour ago by
xiaoleiusc
▴ 110 • written 22 months ago by
Amr
▴ 140
8
votes
4
replies
5.0k
views
How to match and reorder these vectors in R
R
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
MAPK
★ 2.0k
8
votes
9
replies
3.5k
views
Forum:
Web Development for Bioinformatics
studies
advice
career
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
edsanhu
▴ 10
8
votes
4
replies
3.9k
views
Tool:
Avalanche Workbench - Automated & visual data analysis (NCBI eSearch, eLink, eFetch, Get genome, Blast)
ncbi
software
sequence
data-mining
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
BioApps
▴ 790
8
votes
19
replies
3.2k
views
Make multi-fasta using perl
perl
multi-fasta
fasta
updated 2 hours ago by
Ram
38k • written 7.8 years ago by
sun.nation
▴ 130
7
votes
6
replies
1.0k
views
7 follow
batch renaming FASTQ files
fastq
rename
batch
updated 19 hours ago by
shenwei356
7.8k • written 23 months ago by
amitpande74
▴ 20
7
votes
4
replies
4.9k
views
Sliding window using gene position file
RNA-seq
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
burnsro
▴ 20
7
votes
17
replies
3.2k
views
6 follow
awk filtering annovar txt files
awk
annovar
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
basalganglia
▴ 40
7
votes
4
replies
1.4k
views
R programming: Merge tables
R
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
MAPK
★ 2.0k
6
votes
6
replies
302
views
command line - how to change name of multiple files at the same time
bash
line
command
script
updated 18 hours ago by
shenwei356
7.8k • written 1 day ago by
tiziana
• 0
6
votes
5
replies
709
views
Tool:
pyCirclize - Circular visualization in Python
visualization
circos
matplotlib
genome
python
updated 16 hours ago by
Jimmy
• 0 • written 7 weeks ago by
moshi
▴ 90
6
votes
11
replies
2.4k
views
Publicly available somatic variant calls for kidney cancer using WGS
somatic-variants
WGS
kidney-cancer
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
tralynca
▴ 50
6
votes
16
replies
6.4k
views
14 follow
Edgeredef Failed When Running Repeatmodeler
repeatmodeler
updated 2 hours ago by
Ram
38k • written 12.0 years ago by
Daniel Standage
4.1k
6
votes
2
replies
127
views
Seurat or Bioconductor for single cell RNA seq
single-cell
bioconductor
seurat
RNAseq
updated 4 hours ago by
Basti
★ 1.3k • written 5 hours ago by
Sandra
▴ 10
6
votes
4
replies
3.0k
views
How to distinguish protein isoforms using biomaRt?
biomaRt
R
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
richierocks
▴ 10
6
votes
2
replies
3.5k
views
Is it possible to get local blast output directly in Biopython, without making and reading an XML file?
blast
biopython
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
atapee
▴ 10
6
votes
3
replies
13k
views
fastq-dump split-spot and skip-technical
fastq-dump
split-spot
skip-technical
updated 5 hours ago by
Larissa Graciano
• 0 • written 7.0 years ago by
Shicheng Guo
★ 9.2k
6
votes
3
replies
3.8k
views
Sample ORTHOMCL run on my Fasta file.
orthomcl-clustering
genome
orthoMCL
sequence
updated 23 hours ago by
Ram
38k • written 7.8 years ago by
Naren
▴ 960
5
votes
5
replies
3.5k
views
Tool for Venn Diagram
protein
sequencing
genome
updated 21 hours ago by
Ram
38k • written 7.8 years ago by
div
▴ 60
5
votes
7
replies
2.0k
views
Transcriptome reconstruction from both short reads and long sequences
Mapping
BAM
SAM
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
Prakki Rama
★ 2.6k
5
votes
3
replies
2.6k
views
How to get simply the sequence between two positions (start-end) in a specific chromosome using Biomart?
Biomart
sequence
updated 21 hours ago by
Ram
38k • written 7.8 years ago by
Zakaria Benmounah
▴ 50
5
votes
13
replies
2.8k
views
Snipsift synonymous variant extraction
filtering
snipsift
updated 3 hours ago by
Ram
38k • written 7.8 years ago by
basalganglia
▴ 40
4
votes
12
replies
359
views
Subbmission Data
submission
in
RNA-seq
data
paper
updated 1 hour ago by
seidel
10k • written 1 day ago by
GiV17
▴ 40
4
votes
2
replies
3.4k
views
Beginner pymol user
pymol
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
m.saola
▴ 20
4
votes
3
replies
5.0k
views
How to calculate connectivity score for a compound in connectivity map O2?
connectivity-map
cmap
connectivity-score
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
Zhilong Jia
★ 2.1k
4
votes
3
replies
8.2k
views
Where to download latest TCGA MAF files?
sequencing
genome
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
ckr123
▴ 10
4
votes
3
replies
1.8k
views
How to define the gene value if a gene is represented by multiple probe sets
gene-value
cel
probe-id
updated 21 hours ago by
Ram
38k • written 7.8 years ago by
zero_hsy
▴ 110
4
votes
11
replies
2.4k
views
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 2 hours ago by
Juke34
7.5k • written 2.8 years ago by
William
★ 5.1k
3
votes
3
replies
145
views
How to map and annotate gene symbols to gene type?
Ensembl
RefSeq
UCSC
biomart
RNA-Seq
updated 16 hours ago by
GenoMax
125k • written 17 hours ago by
mohammedtoufiq91
▴ 170
3
votes
3
replies
3.4k
views
Linc and miRNA in GTF file
GTF
lincRNA
miRNA
lncRNA
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
Sandeep
▴ 260
3
votes
1
reply
1.4k
views
skewed cuffdiff result
RNA-Seq
sequencing
gene
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
kint1007
▴ 20
3
votes
4
replies
4.1k
views
Getting Protein Information from NCBI Gene ID
protein
ncbi-id
NCBI
python
gene
updated 20 hours ago by
Ram
38k • written 7.8 years ago by
joseph.orlando
• 0
3
votes
3
replies
4.8k
views
VCF format conventions for multi-sample vs. single-sample data
1000genomes
vcf
snpeff
updated 23 hours ago by
Ram
38k • written 7.8 years ago by
bberns
▴ 20
3
votes
3
replies
8.3k
views
Trimming read length & quality in a FASTQ file
RNA-Seq
next-gen
updated 2 hours ago by
Ram
38k • written 7.8 years ago by
ChIP
▴ 600
3
votes
7
replies
6.4k
views
How to link UCSC transcripts ids to protein ids using bioconductor ?
genome
sequence
gene
Forum
R
updated 21 hours ago by
Ram
38k • written 8.7 years ago by
Aurelie MLB
▴ 360
3
votes
2
replies
8.4k
views
HTA 2.0 (Human Transcriptome Array 2.0 - Affymetrix) analysis tools/pipeline?
hta 2.0
affymetrix
R
analysis
updated 20 hours ago by
Ram
38k • written 8.6 years ago by
Rm
8.2k
2
votes
0
replies
2.1k
views
Four Gamete Test
four-gamete-test
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
thakurshalabh
▴ 60
2
votes
5
replies
3.1k
views
Do you have abnormally long introns in your RNA Seq alignment? How do you get rid of them?
alignment
RNA-Seq
STAR
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
cyril-cros
▴ 940
2
votes
4
replies
305
views
Issues With Using Singularity In Order To Run Software "quested access to the resource is denied"
Singularity
updated 11 hours ago by
ATpoint
69k • written 1 day ago by
Indira
• 0
167 results • Page
1 of 4
Recent Votes
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date
Comment: Subbmission Data
Comment: Subbmission Data
Answer: Subbmission Data
Answer: how I can install lumi, plier, simpleaffy, oligo classes, LMGene and siggens pac
Comment: Bacterial metatranscriptomics with DESEQ2?
C: How to extend contigs from single-end reads?
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★ 2.2k
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mathavanbioinfo
▴ 70
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Recent Replies
Comment: Subbmission Data
by
seidel
10k
GEO allows you to keep your data private for up to three years, AND has a mechanism where you can share it with reviewers without it being …
Comment: PyMOL: Gaps in protein structure yet shown by the sequence
by
spence.lank
▴ 10
The PDB ID for this structure is 7DK3 and the literature is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775788/
Comment: Problem with tximport and plasmodium falciparum
by
ATpoint
69k
You do not do what I suggested above.
Comment: Relative frequencies of the nucleotides in Fasta files
by
xiaoleiusc
▴ 110
Hi, Hugo, I acknowledged you in my paper recently published. Thanks for your help! Xiao PS, paper link https://elifesciences.org/articles/8…
Comment: Stringtie prepDE.py script
by
Buffo
★ 2.0k
from the manual: -i a folder containing all sample sub-directories, or a text file with sample ID and path to its GTF file on each lin…
Comment: Using Entrez Utilities to query the Nucleotide database by collection_date
by
anomalous.lexeme
• 0
That looks pretty useful. I'll give that a try as well. Thank you very kindly for the help.
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Juke34
7.5k
This script does not exist anymore in recent releases. Without any example I cannot help.
Comment: Create de novo repeat library
by
evoecogen
▴ 20
Are there any alternatives to ProtExcluder? I suddenly started to have problems with v1.2: The files blastx.out.fnolowm50seqm and blastx.o…
Comment: Find corresponding branch from gene tree in species tree
by
Charlotte West
▴ 40
Following your suggestion I've been playing around with Notung and seems like its got a lot of great features. I ran: ``` java -jar notung …
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Lisa
• 0
thanks for your help
Comment: docker build Command Works Yet It Does Not Create A Docker Container
by
Indira
• 0
So - I am trying to get around proxy issues but essentially installing required packages in a docker/sif then trying to use that to run an …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Ram
38k
Do not add answers unless you're **answering** the top level question. Use `Add Comment` or `Add Reply` instead as appropriate. I've moved …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
BioinfoBee
• 0
@juke34 I tried the agat_sp_gxf_to_gff3.pl to sort the gff3 by their chromosome order but doesn't seems to work. Any suggestions?.
Comment: CNV Prediction Tools
by
Quentin M
▴ 60
Give a try to [CODEX2][1] [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y
Comment: Problem with tximport and plasmodium falciparum
by
bioinfo
▴ 20
Thank you. It does not seem to be that. I changed my script a bit. Now it looks like shown below: mart <- biomaRt::useMart("protists_…
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