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807 results • Page
4 of 17
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3
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1
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1.4k
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Performing Hmmer search against pfam versus UniRef100
hmmer
pfam
alignment
updated 3 days ago by
Ram
39k • written 3.8 years ago by
baverso
• 0
3
votes
0
replies
1.4k
views
Job:
American Museum of Natural History - Bioinformatics Specialist
genomics
updated 3 days ago by
Ram
39k • written 3.8 years ago by
anarechania
▴ 30
3
votes
0
replies
1.3k
views
News:
Analysis of single cell RNA-seq data - Berlin 23 -27 March 2020
scRNA-seq
RNA-Seq
updated 4 days ago by
Ram
39k • written 3.9 years ago by
carlopecoraro2
★ 2.3k
3
votes
7
replies
4.0k
views
Getting Pairwise Sequence Alignment Score With Biopython
biopython
alignment
clustalw
updated 1 hour ago by
Jonathan Lefebre
▴ 70 • written 11.5 years ago by
Lakshmi
• 0
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 4 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
3
votes
0
replies
657
views
News:
::FINAL CALL:: NGS Data Analysis for Beginners - 11-13 December 2019 in Munich, Germany (2 seats left)
NGS
Workshop
updated 16 hours ago by
Ram
39k • written 3.6 years ago by
David Langenberger
9.9k
3
votes
5
replies
1.8k
views
should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential expression analysis
RNA-Seq
rna-seq
updated 22 hours ago by
Kermit
▴ 80 • written 4.2 years ago by
hellocita
▴ 40
3
votes
0
replies
1.1k
views
News:
Nextflow Training Course
Pipeline
Workflow
NEXTFLOW
updated 18 hours ago by
Ram
39k • written 3.7 years ago by
carlopecoraro2
★ 2.3k
3
votes
3
replies
1.4k
views
Error in installation of RandFold 2.0
Linux
rna-seq
Ubuntu
updated 18 hours ago by
Ram
39k • written 3.7 years ago by
akshay_ware
▴ 30
3
votes
2
replies
899
views
Job:
Postdoc in computational and experimental annotation of tRNA-related sequences
qPCR
plant
hybridization
genomics
trna
updated 3 days ago by
Ram
39k • written 3.7 years ago by
Andrzej Zielezinski
11k
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly
alignment
updated 3 days ago by
Ram
39k • written 3.8 years ago by
Palgrave
▴ 110
3
votes
3
replies
1.3k
views
Bridge Amplification error rate and duplicates in NGS
NGS
PCR-duplicates
bridge-pcr
next-gen
updated 4 days ago by
Ram
39k • written 3.9 years ago by
KirGen
▴ 20
3
votes
6
replies
300
views
Salmon Index
transcriptomics
Bulk
RNA-sequencing
updated 6 days ago by
GenoMax
129k • written 6 days ago by
ashleymb1116
• 0
3
votes
2
replies
206
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 4 days ago by
Jeremy Leipzig
21k • written 5 days ago by
JourneyToAbyss
▴ 210
3
votes
0
replies
967
views
Job:
Three PI positions in neurogenomics or neuroscience at VIB-UAntwerp (Belgium)
VIB
neuroscience
genomics
updated 18 hours ago by
Ram
39k • written 3.7 years ago by
WouterDeCoster
47k
2
votes
2
replies
151
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap
deepTools
1 day ago by
Dan
▴ 120
2
votes
3
replies
245
views
Getting species names and taxa id from assembly accession number
efetch
biopython
entrez
updated 23 hours ago by
MirianT_NCBI
▴ 600 • written 1 day ago by
kwhiggins27
▴ 10
2
votes
0
replies
785
views
News:
R/Bioconductor for Mass Spectrometry and Proteomics course in Berlin
R
Proteomics
Bioconductor
updated 3 days ago by
Ram
39k • written 3.8 years ago by
carlopecoraro2
★ 2.3k
2
votes
5
replies
244
views
Embryo transcriptome
database
transcriptome
SRA
updated 14 hours ago by
ATpoint
72k • written 22 hours ago by
firefox91
• 0
2
votes
0
replies
1.3k
views
News:
UCSC Genome Browser JSON API
ucsc
json
api
updated 5 days ago by
Ram
39k • written 3.9 years ago by
Pierre Lindenbaum
154k
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation
mutational signature
updated 4 days ago by
Vincent Laufer
★ 2.9k • written 4.4 years ago by
lzy
▴ 20
2
votes
1
reply
1.4k
views
News:
Meet Dr. Giovanni Marco Dall'Olio
NGS
training
RNA-Seq
updated 6 days ago by
Ram
39k • written 4.2 years ago by
David Langenberger
9.9k
2
votes
0
replies
509
views
News:
Introduction to RMarkdown
R
updated 3 days ago by
Ram
39k • written 3.8 years ago by
carlopecoraro2
★ 2.3k
2
votes
0
replies
739
views
News:
The BioCompute Object App-a-thon is now live!
app-a-thon
pipeline
precisionFDA
updated 6 days ago by
Ram
39k • written 4.1 years ago by
stephens_sarah
▴ 150
2
votes
2
replies
181
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 4 days ago by
Dr William Klubinski
▴ 90 • written 5 days ago by
linnet.roque6
▴ 10
2
votes
3
replies
202
views
Gene enrichment analysis
Go
enrichment
r
gene
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Eliza
• 0
2
votes
2
replies
194
views
I need help with a blast command, please help
linux
blast
updated 21 hours ago by
Ram
39k • written 1 day ago by
neto.pvp
• 0
2
votes
0
replies
869
views
News:
Metagenomics and Metabarcoding Course @ Edinburgh Genomics
metagenomics
metabarcoding
course
workshop
updated 4 days ago by
Ram
39k • written 3.9 years ago by
Edinburgh Genomics Training
▴ 40
2
votes
12
replies
2.8k
views
6 follow
Using RPK counts as DESeq2 input
deseq2
updated 5 days ago by
Ram
39k • written 6.0 years ago by
adityabandla
▴ 30
2
votes
3
replies
411
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 4 days ago by
rfran010
▴ 140 • written 7 days ago by
JACKY
▴ 100
2
votes
1
reply
1.4k
views
Job:
We are seeking a Scientist II/Sr. Scientist in Bioinformatics!
RNA-Seq
updated 6 days ago by
Ram
39k • written 4.2 years ago by
ritsuko.someya
▴ 20
2
votes
3
replies
227
views
NCBI refseq ids to uniprot ids
refseq
Uniprot
updated 6 days ago by
Ram
39k • written 7 days ago by
t.ali
• 0
2
votes
2
replies
6.7k
views
GATK -Xmx4G and -Xmx8G
GATK
HaplotypeCaller
updated 4 days ago by
Ram
39k • written 3.9 years ago by
lovegenetics
▴ 70
2
votes
0
replies
757
views
News:
Course - Landscape Genomics. Berlin
Genomics
R
updated 18 hours ago by
Ram
39k • written 3.7 years ago by
carlopecoraro2
★ 2.3k
2
votes
1
reply
477
views
How to enter bioinformatics programme
career
updated 3 days ago by
Ram
39k • written 3.8 years ago by
wierdrequests
• 0
2
votes
0
replies
2.6k
views
Job:
15 PhD positions in Quantitative Biology, Lausanne, Switzerland
switzerland
phd
quantitative-biology
updated 3 days ago by
Ram
39k • written 3.7 years ago by
Christophe Dessimoz
▴ 740
2
votes
0
replies
724
views
Why are there multiple bax/fastq files associated with my PacBio run?
genome
PacBio
WGS
sequencing
updated 6 days ago by
Ram
39k • written 4.1 years ago by
nickvpinkham
▴ 20
2
votes
7
replies
1.0k
views
How to specify output format in stand alone emboss-SKIPREDUNDANT?
skipredundant
emboss
fasta
updated 6 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
2
votes
4
replies
821
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 17 hours ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
2
votes
3
replies
466
views
ATAC peak-calling: same peak ID across multiple experimental conditions?
Genrich
ATAC
updated 4 days ago by
rfran010
▴ 140 • written 24 days ago by
weimichelles
• 0
2
votes
8
replies
1.2k
views
How to append two fasta files?
unix
fasta
python
updated 5 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
2
votes
2
replies
175
views
Create customized gene annotation file
reference-genome
cellranger
2 days ago by
rhonddaskl
• 0
2
votes
6
replies
1.7k
views
How can I identify cells from Single cell experiment (SCE) using bulk RNA experiment (RNAseq) genes signatures?
RNA-Seq
next-gen
updated 3 days ago by
Ram
39k • written 3.8 years ago by
sofiagreen72211
▴ 30
2
votes
0
replies
1.1k
views
Job:
Ensembl genebuild bioinformatician
gene-annotation
ensembl
genomics
updated 18 hours ago by
Ram
39k • written 3.7 years ago by
Emily
23k
2
votes
0
replies
916
views
News:
#NGSchool2019: Machine Learning for Biomedicine
ngschool
workshop
training
summer-school
next-gen
updated 6 days ago by
Ram
39k • written 4.1 years ago by
kzkedzierska
▴ 290
2
votes
2
replies
3.4k
views
How to download time series expression datasets?
matlab
time-series
microarray
gene-expression
updated 6 days ago by
Ram
39k • written 7.6 years ago by
Andrea
▴ 60
2
votes
6
replies
2.2k
views
6 follow
Job:
Seeking Freelance bioinformatician
association
burden
gwas
updated 5 days ago by
Ram
39k • written 4.0 years ago by
epoceire
• 0
2
votes
5
replies
1.6k
views
NarrowPeak format -Peak field
ChIP-Seq
dnase-seq
bed
updated 4 days ago by
ATpoint
72k • written 2.7 years ago by
kimkes25
▴ 50
2
votes
0
replies
881
views
News:
Summer Courses @ Edinburgh Genomics
workshop
training
courses
python
RNA-Seq
updated 5 days ago by
Ram
39k • written 4.0 years ago by
Edinburgh Genomics Training
▴ 40
2
votes
1
reply
77
views
Visualizing Graph Alignment Format via minigraph
graph
gaf
minigraph
alignment
updated 2 hours ago by
colindaven
4.8k • written 17 hours ago by
ivazirabad
▴ 20
807 results • Page
4 of 17
Recent Votes
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
Comment: Getting Pairwise Sequence Alignment Score With Biopython
C: How does salmon deal with decoy?
A: How does salmon deal with decoy?
A: How does salmon deal with decoy?
Comment: Italicise annotations with pheatmap
Visualizing Graph Alignment Format via minigraph
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Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Sure, here is my json file, I have 8 fastq files: { "atac.title" : “atac)”, "atac.description" : “Encode”, …
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
Yes, you need to log-transform. I've had a good experience using limma for proteomics analyses (limma uses a moderated t-test).
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
by
mattze731
▴ 10
Never mind. Someone had put all the 16S files into the ITS folder and vice versa. After using the 16S dada2 pipeline on the actual 16S file…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴ 70
Dear Alexander, to answer 2) first: This is just a fasta file that you can obtain essentially from every multiple sequence alignment soft…
Comment: Stratified sample assignment for analysis
by
ATpoint
72k
Batches for what? Processing/sequencing, what data are we talking about? If this is indeed paired then you basically must keep samples of a…
Answer: Visualizing Graph Alignment Format via minigraph
by
colindaven
4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis
by
Vincent Laufer
★ 2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq. Generally, your options …
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★ 2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms
by
Alexander
▴ 70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Alexander
▴ 70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments. I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use?
by
fracarb8
▴ 950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software
by
alexandru.bologa.marian
▴ 40
Hi, I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴ 70
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
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